#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_Codon	i_COSMIC_Gene	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_Chromosome_hg18	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Drug_Target	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_End_position_hg18	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_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_Mutation_Status	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_Start_position_hg18	i_TranscriptID	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
LRIG1	26018	hgsc.bcm.edu	37	3	66457849	66457850	+	Frame_Shift_Ins	INS	-	-	CT			TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	-	-	-	CT	-	-	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	g.chr3:66457849_66457850insCT	ENST00000273261.3	-	8	1525_1526	c.1001_1002insAG	c.(1000-1002)agtfs	p.S334fs	LRIG1_ENST00000496559.2_5'Flank|LRIG1_ENST00000383703.3_Frame_Shift_Ins_p.S334fs	NM_015541.2	NP_056356.2	Q96JA1	LRIG1_HUMAN	leucine-rich repeats and immunoglobulin-like domains 1	334					innervation (GO:0060384)|otolith morphogenesis (GO:0032474)|sensory perception of sound (GO:0007605)	integral component of membrane (GO:0016021)		p.S334fs*39(1)		NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|prostate(1)|skin(4)|stomach(4)|urinary_tract(1)	42		Lung NSC(201;0.0101)		BRCA - Breast invasive adenocarcinoma(55;0.00047)		GACGCAGGACACTCAGGCTGCT	0.589																																					p.S334fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.1002_1003insAG	3						.																																			66540540	SO:0001589	frameshift_variant	26018	exon8			AB050468	CCDS33783.1	3p14	2013-01-14			ENSG00000144749	ENSG00000144749		"""Immunoglobulin superfamily / I-set domain containing"""	17360	protein-coding gene	gene with protein product	"""ortholog of mouse integral membrane glycoprotein LIG-1"", ""leucine-rich repeat protein LRIG1"""	608868				11414704, 12234026	Standard	NM_015541		Approved	LIG-1, DKFZP586O1624, LIG1	uc003dmx.3	Q96JA1	OTTHUMG00000158727	ENST00000273261.3:c.1000_1001dupAG	3.37:g.66457850_66457851dupCT	ENSP00000273261:p.Ser334fs	Somatic		Capture	SOLID	Phase_I	66540539	NM_015541	Q6IQ51|Q96CF9|Q9BYB8|Q9UFI4	Frame_Shift_Ins	INS	ENST00000273261.3	37	CCDS33783.1																																																																																				0.589	LRIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351930.1	NM_015541	
GRM8	2918	hgsc.bcm.edu	37	7	126249446	126249446	+	Silent	SNP	G	G	T	rs769198	byFrequency	TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	g.chr7:126249446G>T	ENST00000339582.2	-	8	2272	c.1464C>A	c.(1462-1464)atC>atA	p.I488I	GRM8_ENST00000444921.2_Silent_p.I488I|GRM8_ENST00000358373.3_Silent_p.I488I|GRM8_ENST00000480995.1_Intron			O00222	GRM8_HUMAN	glutamate receptor, metabotropic 8	488					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|negative regulation of cAMP biosynthetic process (GO:0030818)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of smell (GO:0007608)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)	p.I488I(1)		breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(16)|lung(62)|ovary(5)|pancreas(1)|prostate(1)|skin(14)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(4)	125		Prostate(267;0.186)				TCCAGTGGCCGATGACTTTGT	0.383										HNSCC(24;0.065)																											p.I488I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1464A	7						.						234.0	205.0	215.0					7																	126249446		2203	4300	6503	126036682	SO:0001819	synonymous_variant	2918	exon8				CCDS5794.1, CCDS47696.1	7q31.3-q32.1	2012-08-29			ENSG00000179603	ENSG00000179603		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4600	protein-coding gene	gene with protein product		601116				8824806	Standard	NM_000845		Approved	GLUR8, GPRC1H, mGlu8, MGLUR8	uc003vlr.2	O00222	OTTHUMG00000022888	ENST00000339582.2:c.1464C>A	7.37:g.126249446G>T		Somatic		Capture	SOLID	Phase_I	126036682	NM_001127323	A4D0Y3|B0FZ74|B0M0L0|O15493|O95945|O95946|Q3MIV9|Q52M02|Q6J165	Silent	SNP	ENST00000339582.2	37	CCDS5794.1																																																																																				0.383	GRM8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059209.4		
SDK1	221935	hgsc.bcm.edu	37	7	3991520	3991520	+	Missense_Mutation	SNP	C	C	T	rs557260722	byFrequency	TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	g.chr7:3991520C>T	ENST00000404826.2	+	7	1257	c.1118C>T	c.(1117-1119)cCg>cTg	p.P373L	SDK1_ENST00000389531.3_Missense_Mutation_p.P373L	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	373	Ig-like C2-type 3.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.P373L(1)		NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		GCTTTTGAACCGGCCAGGGCG	0.602													C|||	2	0.000399361	0.0008	0.0	5008	,	,		16639	0.001		0.0	False		,,,				2504	0.0				p.P373L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1118T	7						.						32.0	36.0	35.0					7																	3991520		2203	4300	6503	3958046	SO:0001583	missense	221935	exon7			AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	19307	protein-coding gene	gene with protein product		607216	"""sidekick homolog 1 (chicken)"", ""sidekick homolog 1, cell adhesion molecule (chicken)"""			12230981, 17307840, 15213259	Standard	NM_001079653		Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000404826.2:c.1118C>T	7.37:g.3991520C>T	ENSP00000385899:p.Pro373Leu	Somatic		Capture	SOLID	Phase_I	3958046	NM_152744	Q8TEN9|Q8TEP5|Q96N44	Missense_Mutation	SNP	ENST00000404826.2	37	CCDS34590.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.35|16.35	3.099680|3.099680	0.56183|0.56183	.|.	.|.	ENSG00000146555|ENSG00000146555	ENST00000404826;ENST00000389531|ENST00000426596	T;T|.	0.61392|.	0.11;0.13|.	4.87|4.87	4.87|4.87	0.63330|0.63330	Immunoglobulin subtype (1);|.	0.392882|.	0.24111|.	N|.	0.041451|.	T|T	0.69459|0.69459	0.3113|0.3113	L|L	0.54323|0.54323	1.7|1.7	0.80722|0.80722	D|D	1|1	P|.	0.47962|.	0.903|.	B|.	0.42653|.	0.394|.	T|T	0.67624|0.67624	-0.5623|-0.5623	10|5	0.52906|.	T|.	0.07|.	.|.	16.5463|16.5463	0.84446|0.84446	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	373|.	Q7Z5N4|.	SDK1_HUMAN|.	L|W	373|92	ENSP00000385899:P373L;ENSP00000374182:P373L|.	ENSP00000374182:P373L|.	P|R	+|+	2|1	0|2	SDK1|SDK1	3958046|3958046	0.648000|0.648000	0.27313|0.27313	0.186000|0.186000	0.23195|0.23195	0.044000|0.044000	0.14063|0.14063	5.850000|5.850000	0.69473|0.69473	2.410000|2.410000	0.81850|0.81850	0.655000|0.655000	0.94253|0.94253	CCG|CGG		0.602	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744	
FAM126A	84668	hgsc.bcm.edu	37	7	22985434	22985434	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	g.chr7:22985434G>A	ENST00000432176.2	-	11	1572	c.1340C>T	c.(1339-1341)gCg>gTg	p.A447V	FAM126A_ENST00000498833.1_5'Flank|FAM126A_ENST00000409923.1_3'UTR	NM_032581.3	NP_115970.2	Q9BYI3	HYCCI_HUMAN	family with sequence similarity 126, member A	447					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)	p.A447V(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(8)|urinary_tract(2)	23						AAATACAGTCGCTGCGGTCTT	0.468																																					p.A447V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1340T	7						.						94.0	88.0	90.0					7																	22985434		2203	4300	6503	22951959	SO:0001583	missense	84668	exon11			BC018710	CCDS5377.1	7p15.3	2008-10-02			ENSG00000122591	ENSG00000122591			24587	protein-coding gene	gene with protein product	"""down regulated by Ctnnb1, a"""	610531				10910037, 16951682	Standard	NM_032581		Approved	DRCTNNB1A, HCC, HYCC1, hyccin	uc003svm.4	Q9BYI3	OTTHUMG00000128435	ENST00000432176.2:c.1340C>T	7.37:g.22985434G>A	ENSP00000403396:p.Ala447Val	Somatic		Capture	SOLID	Phase_I	22951959	NM_032581	A4D145|Q6N010|Q75MR4|Q7LDZ4|Q96MX1|Q96NQ6	Missense_Mutation	SNP	ENST00000432176.2	37	CCDS5377.1	.	.	.	.	.	.	.	.	.	.	G	13.68	2.310395	0.40895	.	.	ENSG00000122591	ENST00000432176	T	0.78003	-1.14	6.16	6.16	0.99307	.	0.273852	0.45867	D	0.000321	T	0.69468	0.3114	N	0.22421	0.69	0.80722	D	1	B	0.28208	0.203	B	0.20184	0.028	T	0.66344	-0.5947	10	0.72032	D	0.01	1.8985	20.8598	0.99761	0.0:0.0:1.0:0.0	.	447	Q9BYI3	HYCCI_HUMAN	V	447	ENSP00000403396:A447V	ENSP00000403396:A447V	A	-	2	0	FAM126A	22951959	0.815000	0.29118	0.015000	0.15790	0.910000	0.53928	5.462000	0.66707	2.937000	0.99478	0.650000	0.86243	GCG		0.468	FAM126A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250230.1	NM_032581	
WBSCR17	64409	hgsc.bcm.edu	37	7	70886058	70886058	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	g.chr7:70886058G>A	ENST00000333538.5	+	5	1563	c.929G>A	c.(928-930)tGg>tAg	p.W310*	WBSCR17_ENST00000498380.2_3'UTR	NM_022479.1	NP_071924.1	Q6IS24	GLTL3_HUMAN	Williams-Beuren syndrome chromosome region 17	310					protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.W310*(1)		NS(5)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(7)|large_intestine(22)|lung(45)|ovary(2)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	100		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)				CCAAAAGACTGGTGGGACGCC	0.577																																					p.W310X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G929A	7						.						66.0	67.0	67.0					7																	70886058		2203	4300	6503	70523994	SO:0001587	stop_gained	64409	exon5			AF410457	CCDS5540.1	7q11.23	2014-03-13			ENSG00000185274	ENSG00000185274		"""Glycosyltransferase family 2 domain containing"""	16347	protein-coding gene	gene with protein product	"""polypeptide N-acetylgalactosaminyltransferase-like 3"", ""polypeptide GalNAc transferase 3"""	615137				12073013, 15744064, 22787146	Standard	NM_022479		Approved	GALNTL3, GalNAc-T5L	uc003tvy.4	Q6IS24	OTTHUMG00000129783	ENST00000333538.5:c.929G>A	7.37:g.70886058G>A	ENSP00000329654:p.Trp310*	Somatic		Capture	SOLID	Phase_I	70523994	NM_022479	Q8NFV9|Q9NTA8	Nonsense_Mutation	SNP	ENST00000333538.5	37	CCDS5540.1	.	.	.	.	.	.	.	.	.	.	G	45	11.478975	0.99566	.	.	ENSG00000185274	ENST00000333538	.	.	.	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	.	18.0015	0.89199	0.0:0.0:1.0:0.0	.	.	.	.	X	310	.	ENSP00000329654:W310X	W	+	2	0	WBSCR17	70523994	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.476000	0.97823	2.490000	0.84030	0.557000	0.71058	TGG		0.577	WBSCR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252006.1	NM_022479	
LRGUK	136332	hgsc.bcm.edu	37	7	133884047	133884047	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	g.chr7:133884047G>A	ENST00000285928.2	+	14	1690	c.1621G>A	c.(1621-1623)Gag>Aag	p.E541K		NM_144648.1	NP_653249.1	Q96M69	LRGUK_HUMAN	leucine-rich repeats and guanylate kinase domain containing	541	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|kinase activity (GO:0016301)	p.E541K(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(23)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	49						GGAAAAATATGAGGGATATTT	0.363																																					p.E541K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1621A	7						.						105.0	113.0	110.0					7																	133884047		2203	4300	6503	133534587	SO:0001583	missense	136332	exon14			AK057348	CCDS5830.1	7q33	2006-10-27			ENSG00000155530	ENSG00000155530			21964	protein-coding gene	gene with protein product							Standard	NM_144648		Approved	FLJ32786	uc003vrm.1	Q96M69	OTTHUMG00000155320	ENST00000285928.2:c.1621G>A	7.37:g.133884047G>A	ENSP00000285928:p.Glu541Lys	Somatic		Capture	SOLID	Phase_I	133534587	NM_144648	Q2M3I1	Missense_Mutation	SNP	ENST00000285928.2	37	CCDS5830.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.505703	0.85282	.	.	ENSG00000155530	ENST00000285928	T	0.42131	0.98	6.11	6.11	0.99139	Guanylate kinase/L-type calcium channel (1);Guanylate kinase (2);	0.069446	0.64402	D	0.000011	T	0.49575	0.1565	M	0.67700	2.07	0.35099	D	0.765028	P	0.45240	0.854	P	0.46144	0.505	T	0.62039	-0.6938	10	0.49607	T	0.09	-29.3253	14.4982	0.67704	0.0703:0.0:0.9297:0.0	.	541	Q96M69	LRGUK_HUMAN	K	541	ENSP00000285928:E541K	ENSP00000285928:E541K	E	+	1	0	LRGUK	133534587	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	4.248000	0.58760	2.906000	0.99361	0.655000	0.94253	GAG		0.363	LRGUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339442.1	NM_144648	
APEX1	328	hgsc.bcm.edu	37	14	20924984	20924984	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	g.chr14:20924984C>T	ENST00000216714.3	+	4	672	c.404C>T	c.(403-405)tCc>tTc	p.S135F	APEX1_ENST00000555414.1_Missense_Mutation_p.S135F|OSGEP_ENST00000556252.1_5'Flank|APEX1_ENST00000557365.1_3'UTR|APEX1_ENST00000557054.1_Intron|OSGEP_ENST00000206542.4_5'Flank|APEX1_ENST00000398030.4_Missense_Mutation_p.S135F	NM_001244249.1|NM_001641.3	NP_001231178.1|NP_001632.2	P27695	APEX1_HUMAN	APEX nuclease (multifunctional DNA repair enzyme) 1	135					aging (GO:0007568)|base-excision repair (GO:0006284)|cell redox homeostasis (GO:0045454)|cellular response to cAMP (GO:0071320)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to peptide hormone stimulus (GO:0071375)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA demethylation (GO:0080111)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|negative regulation of smooth muscle cell migration (GO:0014912)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|oxidation-reduction process (GO:0055114)|positive regulation of DNA repair (GO:0045739)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribosome (GO:0005840)|transcription factor complex (GO:0005667)	3'-5' exonuclease activity (GO:0008408)|chromatin DNA binding (GO:0031490)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|double-stranded DNA 3'-5' exodeoxyribonuclease activity (GO:0008311)|endodeoxyribonuclease activity (GO:0004520)|endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)|phosphodiesterase I activity (GO:0004528)|phosphoric diester hydrolase activity (GO:0008081)|poly(A) RNA binding (GO:0044822)|RNA-DNA hybrid ribonuclease activity (GO:0004523)|site-specific endodeoxyribonuclease activity, specific for altered base (GO:0016890)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|uracil DNA N-glycosylase activity (GO:0004844)	p.S135F(1)		breast(2)|endometrium(1)|large_intestine(4)|ovary(2)	9	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;1.09e-07)|all cancers(55;1.19e-06)	GBM - Glioblastoma multiforme(265;0.0224)|READ - Rectum adenocarcinoma(17;0.193)	Lucanthone(DB04967)	GGCCTGCTTTCCCGCCAGTGC	0.498								Other BER factors																													p.S135F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C404T	14						.						42.0	42.0	42.0					14																	20924984		2203	4300	6503	19994824	SO:0001583	missense	328	exon4			X59764	CCDS9550.1	14q11.2	2008-02-05	2002-09-11	2002-09-13	ENSG00000100823	ENSG00000100823	4.2.99.18		587	protein-coding gene	gene with protein product		107748	"""APEX nuclease (multifunctional DNA repair enzyme)"""	APEX			Standard	NM_001641		Approved	APE, REF1, HAP1, APX, APEN, REF-1, APE-1	uc021rnr.1	P27695	OTTHUMG00000029544	ENST00000216714.3:c.404C>T	14.37:g.20924984C>T	ENSP00000216714:p.Ser135Phe	Somatic		Capture	SOLID	Phase_I	19994824	NM_080648	Q969L5|Q99775	Missense_Mutation	SNP	ENST00000216714.3	37	CCDS9550.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.66|17.66	3.444350|3.444350	0.63178|0.63178	.|.	.|.	ENSG00000100823|ENSG00000100823	ENST00000438886|ENST00000555414;ENST00000216714;ENST00000553681;ENST00000557344;ENST00000398030;ENST00000555839;ENST00000556054;ENST00000557592;ENST00000557150	.|D;D;D;D;D;D;D;D;D	.|0.84298	.|-1.83;-1.83;-1.83;-1.83;-1.83;-1.83;-1.83;-1.83;-1.83	5.79|5.79	5.79|5.79	0.91817|0.91817	.|Endonuclease/exonuclease/phosphatase (2);	.|0.151079	.|0.64402	.|D	.|0.000014	D|D	0.93462|0.93462	0.7914|0.7914	M|M	0.89715|0.89715	3.055|3.055	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.91635	.|0.999	D|D	0.94230|0.94230	0.7475|0.7475	5|10	.|0.87932	.|D	.|0	.|.	14.4271|14.4271	0.67222|0.67222	0.0:0.8524:0.1476:0.0|0.0:0.8524:0.1476:0.0	.|.	.|135	.|P27695	.|APEX1_HUMAN	S|F	85|135;135;135;135;135;135;135;118;118	.|ENSP00000451979:S135F;ENSP00000216714:S135F;ENSP00000451327:S135F;ENSP00000452137:S135F;ENSP00000381111:S135F;ENSP00000452460:S135F;ENSP00000451170:S135F;ENSP00000451060:S118F;ENSP00000452418:S118F	.|ENSP00000216714:S135F	P|S	+|+	1|2	0|0	APEX1|APEX1	19994824|19994824	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	2.832000|2.832000	0.48152|0.48152	2.733000|2.733000	0.93635|0.93635	0.655000|0.655000	0.94253|0.94253	CCC|TCC		0.498	APEX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073641.3	NM_001641	
DYNC1H1	1778	hgsc.bcm.edu	37	14	102446288	102446288	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	g.chr14:102446288C>T	ENST00000360184.4	+	4	915	c.751C>T	c.(751-753)Cgc>Tgc	p.R251C		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	251	Stem. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)	p.R251C(1)		NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						TGGAGTTAACCGCTGGATCCG	0.348																																					p.R251C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C751T	14						.						88.0	95.0	92.0					14																	102446288		2203	4300	6503	101516041	SO:0001583	missense	1778	exon4			AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"""Cytoplasmic dyneins"""	2961	protein-coding gene	gene with protein product		600112	"""dynein, cytoplasmic, heavy polypeptide 1"""	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.751C>T	14.37:g.102446288C>T	ENSP00000348965:p.Arg251Cys	Somatic		Capture	SOLID	Phase_I	101516041	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Missense_Mutation	SNP	ENST00000360184.4	37	CCDS9966.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.755979	0.89843	.	.	ENSG00000197102	ENST00000360184	T	0.56776	0.44	5.31	5.31	0.75309	Dynein heavy chain, domain-1 (1);	0.050740	0.85682	D	0.000000	T	0.77974	0.4211	M	0.89353	3.025	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.81773	-0.0779	10	0.59425	D	0.04	.	18.9739	0.92728	0.0:1.0:0.0:0.0	.	251	Q14204	DYHC1_HUMAN	C	251	ENSP00000348965:R251C	ENSP00000348965:R251C	R	+	1	0	DYNC1H1	101516041	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	7.461000	0.80834	2.486000	0.83907	0.491000	0.48974	CGC		0.348	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376	
CACNG2	10369	hgsc.bcm.edu	37	22	36983540	36983540	+	Silent	SNP	G	G	A	rs148787239		TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	.			Illumina GAIIx	TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	g.chr22:36983540G>A	ENST00000300105.6	-	2	1248	c.267C>T	c.(265-267)taC>taT	p.Y89Y	CACNG2_ENST00000480002.1_5'Flank	NM_006078.3	NP_006069.1	Q9Y698	CCG2_HUMAN	calcium channel, voltage-dependent, gamma subunit 2	89					membrane depolarization (GO:0051899)|membrane hyperpolarization (GO:0060081)|neuromuscular junction development (GO:0007528)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)	p.Y89Y(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(4)|prostate(1)|skin(1)|urinary_tract(1)	18						TGTCAGCTTCGTAATCTGCAT	0.473													G|||	1	0.000199681	0.0008	0.0	5008	,	,		23298	0.0		0.0	False		,,,				2504	0.0				p.Y89Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C267T	22						.						225.0	189.0	201.0					22																	36983540		2203	4300	6503	35313486	SO:0001819	synonymous_variant	10369	exon2			AF096322	CCDS13931.1	22q13.1	2006-08-01			ENSG00000166862	ENSG00000166862		"""Calcium channel subunits"""	1406	protein-coding gene	gene with protein product		602911					Standard	NM_006078		Approved	stargazin, MGC138502, MGC138504	uc003aps.2	Q9Y698	OTTHUMG00000030612	ENST00000300105.6:c.267C>T	22.37:g.36983540G>A		Somatic		Capture	SOLID	Phase_I	35313486	NM_006078	Q2M1M1|Q5TGT3|Q9UGZ7	Silent	SNP	ENST00000300105.6	37	CCDS13931.1																																																																																				0.473	CACNG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075500.2		
GTPBP1	9567	hgsc.bcm.edu	37	22	39112748	39112748	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	g.chr22:39112748C>T	ENST00000216044.5	+	4	810	c.577C>T	c.(577-579)Cgc>Tgc	p.R193C		NM_004286.4	NP_004277.2	O00178	GTPB1_HUMAN	GTP binding protein 1	193	tr-type G. {ECO:0000255|PROSITE- ProRule:PRU01059}.				GTP catabolic process (GO:0006184)|immune response (GO:0006955)|positive regulation of mRNA catabolic process (GO:0061014)|signal transduction (GO:0007165)	cytoplasmic exosome (RNase complex) (GO:0000177)|cytosol (GO:0005829)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)	p.R193C(1)		endometrium(2)|large_intestine(3)|lung(9)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	18	Melanoma(58;0.04)					AGGCTTTGCCCGCCAGAAACT	0.552																																					p.R193C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C577T	22						.						57.0	56.0	56.0					22																	39112748		2203	4300	6503	37442694	SO:0001583	missense	9567	exon4			U87964	CCDS13977.2	22q13.1	2008-07-01			ENSG00000100226	ENSG00000100226			4669	protein-coding gene	gene with protein product		602245				9070279	Standard	XM_005261857		Approved	GP-1, HSPC018	uc003awg.3	O00178	OTTHUMG00000151002	ENST00000216044.5:c.577C>T	22.37:g.39112748C>T	ENSP00000216044:p.Arg193Cys	Somatic		Capture	SOLID	Phase_I	37442694	NM_004286	Q6IC67	Missense_Mutation	SNP	ENST00000216044.5	37	CCDS13977.2	.	.	.	.	.	.	.	.	.	.	C	22.3	4.277245	0.80580	.	.	ENSG00000100226	ENST00000216044;ENST00000484657	T;T	0.71341	-0.56;-0.56	5.25	4.22	0.49857	Protein synthesis factor, GTP-binding (1);	0.053428	0.85682	D	0.000000	D	0.88381	0.6421	H	0.97214	3.96	0.80722	D	1	D	0.71674	0.998	D	0.72338	0.977	D	0.90553	0.4510	10	0.87932	D	0	.	10.8796	0.46931	0.1471:0.7113:0.1416:0.0	.	193	O00178	GTPB1_HUMAN	C	193;112	ENSP00000216044:R193C;ENSP00000442881:R112C	ENSP00000216044:R193C	R	+	1	0	GTPBP1	37442694	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	4.743000	0.62110	1.186000	0.42985	0.551000	0.68910	CGC		0.552	GTPBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075532.1	NM_004286	
ZNF596	169270	hgsc.bcm.edu	37	8	196070	196070	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	g.chr8:196070G>A	ENST00000398612.1	+	6	1606	c.1223G>A	c.(1222-1224)cGa>cAa	p.R408Q	ZNF596_ENST00000308811.4_Missense_Mutation_p.R408Q|ZNF596_ENST00000320552.2_Missense_Mutation_p.R338Q	NM_001042415.1|NM_001042416.1	NP_001035880.1|NP_001035881.1	Q8TC21	ZN596_HUMAN	zinc finger protein 596	408					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.R408Q(1)		autonomic_ganglia(1)|endometrium(2)|large_intestine(6)|lung(5)	14		all_cancers(2;4.81e-29)|all_epithelial(2;5.03e-19)|Lung NSC(2;8.68e-08)|all_lung(2;1.52e-07)|Ovarian(12;0.00965)|Colorectal(14;0.0367)|all_neural(12;0.0837)|Myeloproliferative disorder(644;0.116)|all_hematologic(2;0.138)|Acute lymphoblastic leukemia(644;0.242)		Epithelial(5;3.77e-18)|all cancers(2;5.2e-17)|OV - Ovarian serous cystadenocarcinoma(5;5.37e-09)|BRCA - Breast invasive adenocarcinoma(11;1.7e-06)|Colorectal(2;6.51e-05)|READ - Rectum adenocarcinoma(2;0.0276)|COAD - Colon adenocarcinoma(149;0.0702)		GACCTCAGACGACATGAGAGA	0.438																																					p.R408Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1223A	8						.						110.0	98.0	102.0					8																	196070		2203	4300	6503	186070	SO:0001583	missense	169270	exon6			BC026190	CCDS5951.2	8p23.3	2013-01-08			ENSG00000172748	ENSG00000172748		"""Zinc fingers, C2H2-type"", ""-"""	27268	protein-coding gene	gene with protein product						12477932	Standard	NM_001287256		Approved		uc003wot.3	Q8TC21	OTTHUMG00000086931	ENST00000398612.1:c.1223G>A	8.37:g.196070G>A	ENSP00000381613:p.Arg408Gln	Somatic		Capture	SOLID	Phase_I	186070	NM_001042416	B2R8P4|O95015|Q8N9X0	Missense_Mutation	SNP	ENST00000398612.1	37	CCDS5951.2	.	.	.	.	.	.	.	.	.	.	.	0.786	-0.760449	0.02996	.	.	ENSG00000172748	ENST00000308811;ENST00000320552;ENST00000398612	T;T;T	0.07216	3.21;3.21;3.21	2.62	-0.845	0.10737	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.05135	0.0137	N	0.20328	0.56	0.09310	N	1	D	0.60575	0.988	P	0.47705	0.555	T	0.23726	-1.0180	9	0.10377	T	0.69	.	3.278	0.06906	0.3113:0.0:0.4939:0.1947	.	408	Q8TC21	ZN596_HUMAN	Q	408;338;408	ENSP00000310033:R408Q;ENSP00000318719:R338Q;ENSP00000381613:R408Q	ENSP00000310033:R408Q	R	+	2	0	ZNF596	186070	0.000000	0.05858	0.000000	0.03702	0.066000	0.16364	-3.424000	0.00475	-0.211000	0.10124	0.655000	0.94253	CGA		0.438	ZNF596-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195858.4	NM_173539	
KCNB2	9312	hgsc.bcm.edu	37	8	73848959	73848959	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	g.chr8:73848959G>T	ENST00000523207.1	+	3	1957	c.1369G>T	c.(1369-1371)Gcc>Tcc	p.A457S		NM_004770.2	NP_004761.2	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 2	457					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of smooth muscle contraction (GO:0006940)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)	p.A457S(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(20)|liver(2)|lung(31)|ovary(2)|pancreas(3)|prostate(2)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	85	Breast(64;0.137)		Epithelial(68;0.105)		Dalfampridine(DB06637)	CTTAAAAGATGCCTTCGCTCG	0.498																																					p.A457S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1369T	8						.						82.0	87.0	86.0					8																	73848959		2203	4300	6503	74011513	SO:0001583	missense	9312	exon3			U69962	CCDS6209.1	8q13.2	2012-07-05			ENSG00000182674	ENSG00000182674		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6232	protein-coding gene	gene with protein product		607738				9612272, 16382104	Standard	NM_004770		Approved	Kv2.2	uc003xzb.3	Q92953	OTTHUMG00000164498	ENST00000523207.1:c.1369G>T	8.37:g.73848959G>T	ENSP00000430846:p.Ala457Ser	Somatic		Capture	SOLID	Phase_I	74011513	NM_004770	Q7Z7D0|Q9BXD3	Missense_Mutation	SNP	ENST00000523207.1	37	CCDS6209.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.361295	0.82353	.	.	ENSG00000182674	ENST00000523207	D	0.97455	-4.39	5.74	5.74	0.90152	.	0.000000	0.45361	D	0.000374	D	0.97720	0.9252	M	0.68952	2.095	0.80722	D	1	P	0.51537	0.946	P	0.55161	0.77	D	0.98038	1.0380	10	0.66056	D	0.02	.	19.91	0.97023	0.0:0.0:1.0:0.0	.	457	Q92953	KCNB2_HUMAN	S	457	ENSP00000430846:A457S	ENSP00000430846:A457S	A	+	1	0	KCNB2	74011513	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	9.869000	0.99810	2.702000	0.92279	0.655000	0.94253	GCC		0.498	KCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378998.1	NM_004770	
RNF19A	25897	hgsc.bcm.edu	37	8	101272206	101272206	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	.			Illumina GAIIx	TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	g.chr8:101272206C>A	ENST00000519449.1	-	10	2018	c.1702G>T	c.(1702-1704)Gta>Tta	p.V568L	RNF19A_ENST00000523255.1_5'UTR|RNF19A_ENST00000341084.2_Missense_Mutation_p.V568L	NM_001280539.1|NM_015435.3	NP_001267468.1|NP_056250.3	Q9NV58	RN19A_HUMAN	ring finger protein 19A, RBR E3 ubiquitin protein ligase	568					microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.V568L(1)		breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(11)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	30	all_cancers(14;3.5e-05)|all_epithelial(15;8.91e-08)|Lung NSC(17;0.000615)|all_lung(17;0.00166)		Epithelial(11;3.06e-11)|all cancers(13;5.78e-09)|OV - Ovarian serous cystadenocarcinoma(57;2.24e-05)|STAD - Stomach adenocarcinoma(118;0.0525)			TCTTTCTGTACATCTGCTTGT	0.378																																					p.V568L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1702T	8						.						132.0	110.0	117.0					8																	101272206		2203	4300	6503	101341382	SO:0001583	missense	25897	exon10			AB029316	CCDS6286.1	8q22	2013-10-03	2013-10-03	2007-08-20		ENSG00000034677		"""RING-type (C3HC4) zinc fingers"""	13432	protein-coding gene	gene with protein product		607119	"""ring finger protein 19"", ""ring finger protein 19A"", ""ring finger protein 19A, E3 ubiquitin protein ligase"""	RNF19		11237715, 10976766	Standard	NM_183419		Approved	dorfin, DKFZp566B1346	uc003yjj.1	Q9NV58		ENST00000519449.1:c.1702G>T	8.37:g.101272206C>A	ENSP00000428968:p.Val568Leu	Somatic		Capture	SOLID	Phase_I	101341382	NM_015435	A3KCU9|Q52LG1|Q9H5H9|Q9H8M8|Q9UFG0|Q9UFX6|Q9Y4Y1	Missense_Mutation	SNP	ENST00000519449.1	37	CCDS6286.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.887381	0.91814	.	.	ENSG00000034677	ENST00000519449;ENST00000341084	D;D	0.87966	-2.32;-2.32	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	D	0.91181	0.7222	L	0.43923	1.385	0.80722	D	1	D	0.64830	0.994	D	0.72625	0.978	D	0.90587	0.4534	10	0.45353	T	0.12	.	19.1074	0.93301	0.0:1.0:0.0:0.0	.	568	Q9NV58	RN19A_HUMAN	L	568	ENSP00000428968:V568L;ENSP00000342667:V568L	ENSP00000342667:V568L	V	-	1	0	RNF19A	101341382	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.078000	0.71282	2.592000	0.87571	0.643000	0.83706	GTA		0.378	RNF19A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380004.1	NM_015435	
KPRP	448834	hgsc.bcm.edu	37	1	152733156	152733156	+	Silent	SNP	C	C	T	rs371632676		TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	g.chr1:152733156C>T	ENST00000606109.1	+	1	1120	c.1092C>T	c.(1090-1092)ggC>ggT	p.G364G	KPRP_ENST00000368773.1_Silent_p.G364G			Q5T749	KPRP_HUMAN	keratinocyte proline-rich protein	364	Pro-rich.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)		p.G364G(2)		NS(1)|breast(1)|endometrium(9)|kidney(1)|large_intestine(10)|lung(21)|ovary(6)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCTCCTGGGGCGCCTCCTGCC	0.662																																					p.G364G												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C1092T	1						.	C		0,4406		0,0,2203	56.0	59.0	58.0		1092	-7.5	0.0	1		58	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	KPRP	NM_001025231.1		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		364/580	152733156	2,13004	2203	4300	6503	150999780	SO:0001819	synonymous_variant	448834	exon2			AY960854	CCDS30862.1	1q21.3	2008-02-05	2007-02-02	2006-12-07	ENSG00000203786	ENSG00000203786			31823	protein-coding gene	gene with protein product		613260	"""chromosome 1 open reading frame 45"""	C1orf45		16297201	Standard	NM_001025231		Approved		uc001fal.1	Q5T749	OTTHUMG00000012402	ENST00000606109.1:c.1092C>T	1.37:g.152733156C>T		Somatic		Capture	SOLID	Phase_I	150999780	NM_001025231		Silent	SNP	ENST00000606109.1	37	CCDS30862.1																																																																																				0.662	KPRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034522.2	NM_001025231	
FCRL3	115352	hgsc.bcm.edu	37	1	157666077	157666077	+	Silent	SNP	G	G	A			TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	.			Illumina GAIIx	TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	g.chr1:157666077G>A	ENST00000368184.3	-	7	1176	c.885C>T	c.(883-885)acC>acT	p.T295T	FCRL3_ENST00000473231.1_5'UTR|FCRL3_ENST00000368186.5_Silent_p.T295T|RP11-367J7.3_ENST00000453692.1_RNA	NM_052939.3	NP_443171.2	Q96P31	FCRL3_HUMAN	Fc receptor-like 3	295	Ig-like C2-type 4.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.T295T(1)		autonomic_ganglia(1)|breast(3)|endometrium(7)|kidney(1)|large_intestine(13)|lung(31)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)	69	all_hematologic(112;0.0378)					GCTGCCCTCCGGTGGGCCGGA	0.517																																					p.T295T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C885T	1						.						95.0	91.0	93.0					1																	157666077		2203	4300	6503	155932701	SO:0001819	synonymous_variant	115352	exon7			AF459027	CCDS1167.1	1q21-q22	2013-01-11			ENSG00000160856	ENSG00000160856		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	18506	protein-coding gene	gene with protein product		606510				11493702, 12014205	Standard	XR_241065		Approved	FCRH3, IRTA3, IFGP3, SPAP2a, SPAP2, SPAP2b, SPAP2c, SPAP2d, SPAP2e, CD307c	uc001frb.3	Q96P31	OTTHUMG00000019400	ENST00000368184.3:c.885C>T	1.37:g.157666077G>A		Somatic		Capture	SOLID	Phase_I	155932701	NM_052939	A0N0M4|A8MTH7|D3DVD2|Q5VXZ8|Q8N6S2|Q96LA4|Q96P27|Q96P28|Q96P29|Q96P30	Silent	SNP	ENST00000368184.3	37	CCDS1167.1																																																																																				0.517	FCRL3-006	NOVEL	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051419.2	NM_052939	
LRRC8D	55144	hgsc.bcm.edu	37	1	90400539	90400539	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	g.chr1:90400539G>A	ENST00000337338.5	+	3	2319	c.1912G>A	c.(1912-1914)Gct>Act	p.A638T	LRRC8D_ENST00000394593.3_Missense_Mutation_p.A638T	NM_001134479.1	NP_001127951.1	Q7L1W4	LRC8D_HUMAN	leucine rich repeat containing 8 family, member D	638					ion transport (GO:0006811)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.A638T(1)		breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(10)|ovary(2)|skin(1)	29		all_lung(203;0.0894)|Lung NSC(277;0.227)		all cancers(265;0.0109)|Epithelial(280;0.0427)		GATGAATGTCGCTGAGCTGGA	0.403																																					p.A638T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1912A	1						.						68.0	68.0	68.0					1																	90400539		2203	4300	6503	90173127	SO:0001583	missense	55144	exon3			AK001332	CCDS726.1	1p22.2	2008-02-05	2005-06-29	2005-06-29	ENSG00000171492	ENSG00000171492			16992	protein-coding gene	gene with protein product		612890	"""leucine rich repeat containing 5"""	LRRC5			Standard	NM_018103		Approved	FLJ10470	uc001dnn.3	Q7L1W4	OTTHUMG00000010583	ENST00000337338.5:c.1912G>A	1.37:g.90400539G>A	ENSP00000338887:p.Ala638Thr	Somatic		Capture	SOLID	Phase_I	90173127	NM_001134479	D3DT29|Q6UWB2|Q9NVW3	Missense_Mutation	SNP	ENST00000337338.5	37	CCDS726.1	.	.	.	.	.	.	.	.	.	.	G	1.845	-0.466567	0.04476	.	.	ENSG00000171492	ENST00000337338;ENST00000394593	T;T	0.55413	0.52;0.52	6.07	6.07	0.98685	.	0.058395	0.64402	D	0.000002	T	0.15825	0.0381	N	0.02181	-0.65	0.52501	D	0.999956	B	0.17852	0.024	B	0.17722	0.019	T	0.27054	-1.0085	9	.	.	.	.	20.6439	0.99570	0.0:0.0:1.0:0.0	.	638	Q7L1W4	LRC8D_HUMAN	T	638	ENSP00000338887:A638T;ENSP00000378093:A638T	.	A	+	1	0	LRRC8D	90173127	1.000000	0.71417	0.965000	0.40720	0.995000	0.86356	6.514000	0.73746	2.884000	0.98904	0.655000	0.94253	GCT		0.403	LRRC8D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029203.2	NM_018103	
CD5L	922	hgsc.bcm.edu	37	1	157805848	157805848	+	Silent	SNP	G	G	A			TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	.			Illumina GAIIx	TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	g.chr1:157805848G>A	ENST00000368174.4	-	3	249	c.153C>T	c.(151-153)gaC>gaT	p.D51D	CD5L_ENST00000484609.1_5'UTR	NM_005894.2	NP_005885.1	O43866	CD5L_HUMAN	CD5 molecule-like	51	SRCR 1. {ECO:0000255|PROSITE- ProRule:PRU00196}.				apoptotic process (GO:0006915)|cellular defense response (GO:0006968)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	scavenger receptor activity (GO:0005044)	p.D51D(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(9)|lung(25)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	52	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			TGTCCCAGCCGTCATCACACA	0.622																																					p.D51D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C153T	1						.						114.0	113.0	113.0					1																	157805848		2203	4300	6503	156072472	SO:0001819	synonymous_variant	922	exon3			U82812	CCDS1171.1	1q21-q23	2008-02-05	2006-03-28		ENSG00000073754	ENSG00000073754			1690	protein-coding gene	gene with protein product		602592	"""apoptosis inhibitor 6"", ""CD5 antigen-like (scavenger receptor cysteine rich family)"""	API6		9045627	Standard	NM_005894		Approved	Spalpha	uc001frk.4	O43866	OTTHUMG00000022440	ENST00000368174.4:c.153C>T	1.37:g.157805848G>A		Somatic		Capture	SOLID	Phase_I	156072472	NM_005894	A8K7M5|Q6UX63	Silent	SNP	ENST00000368174.4	37	CCDS1171.1																																																																																				0.622	CD5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058346.1	NM_005894	
OR5F1	338674	hgsc.bcm.edu	37	11	55761363	55761363	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	g.chr11:55761363C>A	ENST00000278409.1	-	1	738	c.739G>T	c.(739-741)Gcc>Tcc	p.A247S		NM_003697.1	NP_003688.1	O95221	OR5F1_HUMAN	olfactory receptor, family 5, subfamily F, member 1	247					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.A247S(1)		endometrium(6)|kidney(1)|large_intestine(11)|liver(1)|lung(33)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	58	Esophageal squamous(21;0.00448)					AGAATTATGGCTGTCAGGTGA	0.493																																					p.A247S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G739T	11						.						88.0	84.0	85.0					11																	55761363		2201	4296	6497	55517939	SO:0001583	missense	338674	exon1			AF065863	CCDS31515.1	11q11	2012-08-09			ENSG00000149133	ENSG00000149133		"""GPCR / Class A : Olfactory receptors"""	8343	protein-coding gene	gene with protein product		608492				9787077	Standard	NM_003697		Approved	OR11-10	uc010riv.2	O95221	OTTHUMG00000166825	ENST00000278409.1:c.739G>T	11.37:g.55761363C>A	ENSP00000278409:p.Ala247Ser	Somatic		Capture	SOLID	Phase_I	55517939	NM_003697	Q495D1|Q6IFB9	Missense_Mutation	SNP	ENST00000278409.1	37	CCDS31515.1	.	.	.	.	.	.	.	.	.	.	C	10.54	1.380223	0.24944	.	.	ENSG00000149133	ENST00000278409	T	0.00164	8.64	2.99	2.99	0.34606	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00356	0.0011	L	0.56199	1.76	0.09310	N	1	D	0.69078	0.997	D	0.72625	0.978	T	0.58842	-0.7565	9	0.56958	D	0.05	.	12.8727	0.57975	0.0:1.0:0.0:0.0	.	247	O95221	OR5F1_HUMAN	S	247	ENSP00000278409:A247S	ENSP00000278409:A247S	A	-	1	0	OR5F1	55517939	0.000000	0.05858	0.022000	0.16811	0.140000	0.21249	0.435000	0.21510	1.417000	0.47077	0.289000	0.19496	GCC		0.493	OR5F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391532.1	NM_003697	
LRP5	4041	hgsc.bcm.edu	37	11	68181165	68181165	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	g.chr11:68181165C>T	ENST00000294304.7	+	12	2618	c.2512C>T	c.(2512-2514)Cgg>Tgg	p.R838W		NM_002335.2	NP_002326.2	O75197	LRP5_HUMAN	low density lipoprotein receptor-related protein 5	838	Beta-propeller 3.				adipose tissue development (GO:0060612)|anatomical structure regression (GO:0060033)|anterior/posterior pattern specification (GO:0009952)|apoptotic process involved in patterning of blood vessels (GO:1902262)|bone marrow development (GO:0048539)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|cell migration involved in gastrulation (GO:0042074)|cell-cell signaling involved in mammary gland development (GO:0060764)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic limb morphogenesis (GO:0030326)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endocytosis (GO:0006897)|extracellular matrix-cell signaling (GO:0035426)|gastrulation with mouth forming second (GO:0001702)|glucose catabolic process (GO:0006007)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|osteoblast development (GO:0002076)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of mitosis (GO:0045840)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of bone remodeling (GO:0046850)|regulation of canonical Wnt signaling pathway (GO:0060828)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|response to peptide hormone (GO:0043434)|retina morphogenesis in camera-type eye (GO:0060042)|retinal blood vessel morphogenesis (GO:0061304)|somatic stem cell maintenance (GO:0035019)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	coreceptor activity (GO:0015026)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.R838W(1)		autonomic_ganglia(1)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(24)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						AGGTCAGGAGCGGGTCGTGAT	0.612																																					p.R838W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2512T	11						.						93.0	71.0	78.0					11																	68181165		2200	4294	6494	67937741	SO:0001583	missense	4041	exon12			AF064548	CCDS8181.1	11q13.4	2014-01-28	2003-03-12		ENSG00000162337	ENSG00000162337		"""Low density lipoprotein receptors"""	6697	protein-coding gene	gene with protein product		603506	"""osteoporosis pseudoglioma syndrome"", ""exudative vitreoretinopathy 1"""	LRP7, OPPG, EVR1		9714764, 10049586	Standard	XM_005273994		Approved	LR3, BMND1, HBM, OPS, OPTA1, VBCH2, EVR4	uc001ont.3	O75197	OTTHUMG00000167570	ENST00000294304.7:c.2512C>T	11.37:g.68181165C>T	ENSP00000294304:p.Arg838Trp	Somatic		Capture	SOLID	Phase_I	67937741	NM_002335	Q96TD6|Q9UES7|Q9UP66	Missense_Mutation	SNP	ENST00000294304.7	37	CCDS8181.1	.	.	.	.	.	.	.	.	.	.	C	16.92	3.256689	0.59321	.	.	ENSG00000162337	ENST00000294304	D	0.96856	-4.15	4.8	3.81	0.43845	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.43919	U	0.000503	D	0.98321	0.9443	M	0.92026	3.265	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.98773	1.0729	10	0.87932	D	0	.	14.8165	0.70039	0.2008:0.7992:0.0:0.0	.	838;838	Q9UES7;O75197	.;LRP5_HUMAN	W	838	ENSP00000294304:R838W	ENSP00000294304:R838W	R	+	1	2	LRP5	67937741	0.216000	0.23585	0.995000	0.50966	0.365000	0.29674	0.709000	0.25734	2.485000	0.83878	0.462000	0.41574	CGG		0.612	LRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395088.1	NM_002335	
HTR3B	9177	hgsc.bcm.edu	37	11	113803799	113803799	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	g.chr11:113803799C>A	ENST00000260191.2	+	6	937	c.680C>A	c.(679-681)gCa>gAa	p.A227E	HTR3B_ENST00000537778.1_Missense_Mutation_p.A216E	NM_006028.4	NP_006019.1	O95264	5HT3B_HUMAN	5-hydroxytryptamine (serotonin) receptor 3B, ionotropic	227					cation transmembrane transport (GO:0098655)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ion channel activity (GO:0005216)|serotonin receptor activity (GO:0004993)|serotonin-activated cation-selective channel activity (GO:0005232)	p.A227E(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(11)	20		all_cancers(61;6.81e-18)|all_epithelial(67;6.67e-11)|all_hematologic(158;4.67e-05)|Melanoma(852;0.000316)|Acute lymphoblastic leukemia(157;0.000976)|Breast(348;0.0101)|Prostate(24;0.0154)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;3.04e-06)|Epithelial(105;1.98e-05)|all cancers(92;0.000201)|OV - Ovarian serous cystadenocarcinoma(223;0.151)	Ergoloid mesylate(DB01049)	GGAGGATTTGCACAGATTCAG	0.483																																					p.A227E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C680A	11						.						115.0	104.0	108.0					11																	113803799		2201	4296	6497	113309009	SO:0001583	missense	9177	exon6			AF080582	CCDS8364.1	11q23.1	2012-05-22	2012-02-03		ENSG00000149305	ENSG00000149305		"""5-HT (serotonin) receptors"", ""Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"""	5298	protein-coding gene	gene with protein product		604654	"""5-hydroxytryptamine (serotonin) receptor 3B"""			9950429, 10521471	Standard	NM_006028		Approved	5-HT3B	uc001pok.3	O95264	OTTHUMG00000168210	ENST00000260191.2:c.680C>A	11.37:g.113803799C>A	ENSP00000260191:p.Ala227Glu	Somatic		Capture	SOLID	Phase_I	113309009	NM_006028	B0YJ23|Q0VJC3	Missense_Mutation	SNP	ENST00000260191.2	37	CCDS8364.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	22.6|22.6	4.309302|4.309302	0.81247|0.81247	.|.	.|.	ENSG00000149305|ENSG00000149305	ENST00000260191;ENST00000537778|ENST00000543092	T;T|.	0.77489|.	-1.1;-1.1|.	5.65|5.65	5.65|5.65	0.86999|0.86999	Neurotransmitter-gated ion-channel ligand-binding (3);|.	0.055765|.	0.64402|.	D|.	0.000001|.	T|T	0.74824|0.74824	0.3767|0.3767	M|M	0.67700|0.67700	2.07|2.07	0.80722|0.80722	D|D	1|1	D;D|.	0.65815|.	0.995;0.993|.	D;D|.	0.69142|.	0.962;0.934|.	T|T	0.71699|0.71699	-0.4514|-0.4514	10|5	0.62326|.	D|.	0.03|.	-12.4157|-12.4157	18.6545|18.6545	0.91445|0.91445	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	216;227|.	O95264-2;O95264|.	.;5HT3B_HUMAN|.	E|N	227;216|156	ENSP00000260191:A227E;ENSP00000443118:A216E|.	ENSP00000260191:A227E|.	A|H	+|+	2|1	0|0	HTR3B|HTR3B	113309009|113309009	1.000000|1.000000	0.71417|0.71417	0.973000|0.973000	0.42090|0.42090	0.667000|0.667000	0.39255|0.39255	6.450000|6.450000	0.73477|0.73477	2.941000|2.941000	0.99782|0.99782	0.655000|0.655000	0.94253|0.94253	GCA|CAC		0.483	HTR3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398842.1	NM_006028	
SYNE1	23345	hgsc.bcm.edu	37	6	152443635	152443635	+	Missense_Mutation	SNP	G	G	A	rs377446250		TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	g.chr6:152443635G>A	ENST00000367255.5	-	146	26931	c.26330C>T	c.(26329-26331)tCc>tTc	p.S8777F	ESR1_ENST00000427531.2_Intron|SYNE1_ENST00000356820.4_Missense_Mutation_p.S3301F|SYNE1_ENST00000448038.1_Missense_Mutation_p.S8729F|SYNE1_ENST00000354674.4_Missense_Mutation_p.S955F|SYNE1_ENST00000539504.1_Missense_Mutation_p.S932F|SYNE1_ENST00000341594.5_Missense_Mutation_p.S8389F|SYNE1_ENST00000265368.4_Missense_Mutation_p.S8777F|SYNE1_ENST00000423061.1_Missense_Mutation_p.S8729F|SYNE1_ENST00000347037.5_5'UTR	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	8777	KASH. {ECO:0000255|PROSITE- ProRule:PRU00385}.				cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.S8777F(2)		NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		AAAGTTGTTGGAGAGGGCACA	0.557										HNSCC(10;0.0054)																											p.S3301F												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C9902T	6						.						119.0	101.0	107.0					6																	152443635		2203	4300	6503	152485328	SO:0001583	missense	23345	exon61			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"""myocyte nuclear envelope protein 1"", ""nuclear envelope spectrin repeat-1"""	608441	"""chromosome 6 open reading frame 98"""	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.26330C>T	6.37:g.152443635G>A	ENSP00000356224:p.Ser8777Phe	Somatic		Capture	SOLID	Phase_I	152485328	NM_015293	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	G	24.3	4.513336	0.85389	.	.	ENSG00000131018	ENST00000367255;ENST00000539504;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000356820;ENST00000313630;ENST00000367247;ENST00000354674	T;T;T;T;T;T;T;T	0.23552	1.9;1.9;1.9;1.9;1.9;1.9;1.9;1.9	5.56	5.56	0.83823	Klarsicht/ANC-1/syne-1 homology (2);	0.141530	0.32655	N	0.005803	T	0.44244	0.1284	M	0.74258	2.255	0.40209	D	0.977601	D;D;P	0.52996	0.957;0.957;0.946	P;P;P	0.61397	0.888;0.888;0.822	T	0.42498	-0.9448	10	0.72032	D	0.01	.	19.5261	0.95208	0.0:0.0:1.0:0.0	.	8777;8777;8729	Q8NF91;E7EQI5;Q8NF91-4	SYNE1_HUMAN;.;.	F	8777;932;8729;8777;8729;8389;3301;962;957;955	ENSP00000356224:S8777F;ENSP00000441052:S932F;ENSP00000396024:S8729F;ENSP00000265368:S8777F;ENSP00000390975:S8729F;ENSP00000341887:S8389F;ENSP00000349276:S3301F;ENSP00000346701:S955F	ENSP00000265368:S8777F	S	-	2	0	SYNE1	152485328	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.634000	0.67833	2.616000	0.88540	0.655000	0.94253	TCC		0.557	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
PRSS35	167681	hgsc.bcm.edu	37	6	84234348	84234348	+	Silent	SNP	C	C	T			TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	.			Illumina GAIIx	TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	g.chr6:84234348C>T	ENST00000369700.3	+	2	1365	c.1188C>T	c.(1186-1188)taC>taT	p.Y396Y	PRSS35_ENST00000536636.1_Silent_p.Y396Y	NM_153362.2	NP_699193.2	Q8N3Z0	PRS35_HUMAN	protease, serine, 35	396	Peptidase S1.					extracellular region (GO:0005576)|mitochondrion (GO:0005739)	serine-type endopeptidase activity (GO:0004252)	p.Y396Y(1)		breast(2)|endometrium(2)|large_intestine(12)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	32		all_cancers(76;0.000113)|Acute lymphoblastic leukemia(125;1.09e-08)|all_hematologic(105;3.12e-05)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0768)		CCCTAAAATACGCCCAGATTT	0.502																																					p.Y396Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1188T	6						.						64.0	47.0	53.0					6																	84234348		2203	4300	6503	84291067	SO:0001819	synonymous_variant	167681	exon3			BC037170	CCDS4999.1	6q14.2	2010-05-12	2004-07-09	2004-07-09	ENSG00000146250	ENSG00000146250		"""Serine peptidases / Serine peptidases"""	21387	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 158"""	C6orf158			Standard	NM_153362		Approved	MGC46520, dJ223E3.1	uc003pjz.3	Q8N3Z0	OTTHUMG00000015113	ENST00000369700.3:c.1188C>T	6.37:g.84234348C>T		Somatic		Capture	SOLID	Phase_I	84291067	NM_001170423	A8K7B3|Q9BQP6	Silent	SNP	ENST00000369700.3	37	CCDS4999.1																																																																																				0.502	PRSS35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041352.1	NM_153362	
C6orf118	168090	hgsc.bcm.edu	37	6	165715721	165715721	+	Silent	SNP	G	G	A			TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	.			Illumina GAIIx	TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	g.chr6:165715721G>A	ENST00000230301.8	-	2	110	c.90C>T	c.(88-90)tgC>tgT	p.C30C	C6orf118_ENST00000543069.1_5'UTR	NM_144980.3	NP_659417.2	Q5T5N4	CF118_HUMAN	chromosome 6 open reading frame 118	30								p.C30C(1)		breast(1)|kidney(2)|large_intestine(9)|liver(1)|lung(21)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	40		Breast(66;6.27e-05)|Ovarian(120;0.0228)|Prostate(117;0.0906)|all_neural(5;0.157)		OV - Ovarian serous cystadenocarcinoma(33;3.23e-18)|BRCA - Breast invasive adenocarcinoma(81;3.11e-06)|GBM - Glioblastoma multiforme(31;0.000313)		CTGGCGTCTCGCAGTGCTTCA	0.527																																					p.C30C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C90T	6						.						66.0	72.0	70.0					6																	165715721		2203	4300	6503	165635711	SO:0001819	synonymous_variant	168090	exon2				CCDS5288.1	6q27	2012-02-06			ENSG00000112539	ENSG00000112539			21233	protein-coding gene	gene with protein product							Standard	NM_144980		Approved	MGC23884, bA85G2.1	uc003qum.4	Q5T5N4	OTTHUMG00000015984	ENST00000230301.8:c.90C>T	6.37:g.165715721G>A		Somatic		Capture	SOLID	Phase_I	165635711	NM_144980	Q8TC11	Silent	SNP	ENST00000230301.8	37	CCDS5288.1																																																																																				0.527	C6orf118-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043026.1	NM_144980	
TP53	7157	hgsc.bcm.edu	37	17	7577547	7577547	+	Missense_Mutation	SNP	C	C	T	rs121912656|rs397516437		TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	g.chr17:7577547C>T	ENST00000269305.4	-	7	923	c.734G>A	c.(733-735)gGc>gAc	p.G245D	TP53_ENST00000359597.4_Missense_Mutation_p.G245D|TP53_ENST00000420246.2_Missense_Mutation_p.G245D|TP53_ENST00000413465.2_Missense_Mutation_p.G245D|TP53_ENST00000455263.2_Missense_Mutation_p.G245D|TP53_ENST00000445888.2_Missense_Mutation_p.G245D|TP53_ENST00000574684.1_5'Flank	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	245	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Interacts with the 53BP2 SH3 domain.|Required for interaction with ZNF385A.		G -> A (in sporadic cancers; somatic mutation).|G -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:1394225, ECO:0000269|PubMed:1978757}.|G -> D (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:2259385}.|G -> E (in a sporadic cancer; somatic mutation).|G -> F (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|G -> H (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|G -> L (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|G -> N (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|G -> R (in sporadic cancers; somatic mutation).|G -> S (in LFS; germline mutation and in sporadic cancers; somatic mutation; dbSNP:rs28934575). {ECO:0000269|PubMed:8829627}.|G -> V (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:2263646}.		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|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)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.G245D(104)|p.G245V(66)|p.G245A(8)|p.0?(8)|p.?(5)|p.G152V(4)|p.G244_M246>V(3)|p.G152D(3)|p.G245N(2)|p.G245H(1)|p.G245L(1)|p.G244fs*17(1)|p.G245F(1)|p.G245E(1)|p.C242_M246>L(1)|p.G245fs*2(1)|p.S241_G245delSCMGG(1)|p.C242fs*98(1)|p.M243fs*18(1)|p.C238_M246delCNSSCMGGM(1)|p.G151_M153>V(1)|p.G245del(1)|p.G245fs*14(1)|p.G245fs*17(1)|p.G245fs*16(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CCGGTTCATGCCGCCCATGCA	0.582		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.G245D	Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	TP53,central_nervous_system,brain,Substitution - Missense,-1	.	219	Substitution - Missense(191)|Whole gene deletion(8)|Deletion - Frameshift(7)|Complex - deletion inframe(5)|Unknown(5)|Deletion - In frame(3)	large_intestine(37)|lung(32)|oesophagus(23)|breast(22)|ovary(18)|upper_aerodigestive_tract(16)|haematopoietic_and_lymphoid_tissue(15)|liver(9)|prostate(7)|stomach(6)|central_nervous_system(6)|skin(6)|biliary_tract(5)|urinary_tract(5)|bone(5)|pancreas(4)|cervix(1)|vulva(1)|endometrium(1)	c.G734A	17	GRCh37	CM010464|CM900209	TP53	M	rs121912656	.						151.0	113.0	126.0					17																	7577547		2203	4300	6503	7518272	SO:0001583	missense	7157	exon7	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.734G>A	17.37:g.7577547C>T	ENSP00000269305:p.Gly245Asp	Somatic		Capture	SOLID	Phase_I	7518272	NM_001126114	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	27.5	4.838149	0.91117	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	D;D;D;D;D;D;D;D	0.99900	-7.62;-7.62;-7.62;-7.62;-7.62;-7.62;-7.62;-7.62	4.62	4.62	0.57501	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99898	0.9951	M	0.91920	3.255	0.80722	A	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	0.999;0.999;1.0;0.999;1.0;1.0	D	0.96045	0.9027	9	0.87932	D	0	-19.4293	15.3618	0.74483	0.0:1.0:0.0:0.0	.	245;245;152;245;245;245	P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;P53_HUMAN;.;.	D	245;245;245;245;245;245;234;152;113;152	ENSP00000410739:G245D;ENSP00000352610:G245D;ENSP00000269305:G245D;ENSP00000398846:G245D;ENSP00000391127:G245D;ENSP00000391478:G245D;ENSP00000425104:G113D;ENSP00000423862:G152D	ENSP00000269305:G245D	G	-	2	0	TP53	7518272	1.000000	0.71417	0.997000	0.53966	0.973000	0.67179	7.609000	0.82925	2.564000	0.86499	0.462000	0.41574	GGC		0.582	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	
UBN1	29855	hgsc.bcm.edu	37	16	4925324	4925324	+	Silent	SNP	C	C	T	rs554942289		TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	g.chr16:4925324C>T	ENST00000396658.4	+	14	3616	c.2913C>T	c.(2911-2913)ggC>ggT	p.G971G	UBN1_ENST00000590769.1_Silent_p.G971G|UBN1_ENST00000545171.1_Silent_p.G971G|UBN1_ENST00000262376.6_Silent_p.G971G	NM_016936.3	NP_058632.2	Q9NPG3	UBN1_HUMAN	ubinuclein 1	971	Ser-rich.				chromatin modification (GO:0016568)|DNA replication-independent nucleosome assembly (GO:0006336)|negative regulation of phosphatase activity (GO:0010923)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|tight junction (GO:0005923)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G971G(1)		NS(1)|endometrium(6)|kidney(4)|large_intestine(10)|lung(12)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38						CCCCTCCAGGCGGTCCAAACG	0.582																																					p.G971G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2913T	16						.						57.0	63.0	61.0					16																	4925324		2197	4300	6497	4865325	SO:0001819	synonymous_variant	29855	exon14			AF108460	CCDS10525.1, CCDS73822.1	16p13.3	2010-11-09			ENSG00000118900	ENSG00000118900			12506	protein-coding gene	gene with protein product		609771				10725330	Standard	XM_005255277		Approved		uc002cyb.3	Q9NPG3	OTTHUMG00000129531	ENST00000396658.4:c.2913C>T	16.37:g.4925324C>T		Somatic		Capture	SOLID	Phase_I	4865325	NM_016936	B7Z6D3|D3DUE8|Q13079|Q9P1P7	Silent	SNP	ENST00000396658.4	37	CCDS10525.1																																																																																				0.582	UBN1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251719.1	NM_016936	
COG4	25839	hgsc.bcm.edu	37	16	70524289	70524289	+	Silent	SNP	G	G	A			TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	.			Illumina GAIIx	TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	g.chr16:70524289G>A	ENST00000323786.5	-	13	1675	c.1654C>T	c.(1654-1656)Ctg>Ttg	p.L552L		NM_001195139.1|NM_015386.2	NP_001182068.1|NP_056201.2	Q9H9E3	COG4_HUMAN	component of oligomeric golgi complex 4	548					Golgi organization (GO:0007030)|Golgi vesicle prefusion complex stabilization (GO:0048213)|protein transport (GO:0015031)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	Golgi transport complex (GO:0017119)|membrane (GO:0016020)		p.L552L(1)		breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(12)|pancreas(1)|prostate(2)	33		Ovarian(137;0.0694)				ACGTTGTTCAGAGTCACCTGG	0.527																																					p.L552L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1654T	16						.						167.0	133.0	145.0					16																	70524289		2198	4300	6498	69081790	SO:0001819	synonymous_variant	25839	exon13			AL050101	CCDS10892.2, CCDS73909.1	16q22.1	2013-09-20			ENSG00000103051	ENSG00000103051		"""Components of oligomeric golgi complex"""	18620	protein-coding gene	gene with protein product		606976				11980916	Standard	NM_015386		Approved	COD1, DKFZP586E1519	uc002ezc.3	Q9H9E3	OTTHUMG00000128515	ENST00000323786.5:c.1654C>T	16.37:g.70524289G>A		Somatic		Capture	SOLID	Phase_I	69081790	NM_015386	B4DMN8|C9JS23|Q96D40|Q9BRF0|Q9BVZ2|Q9H5Y4|Q9Y3W3	Silent	SNP	ENST00000323786.5	37	CCDS10892.2																																																																																				0.527	COG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250326.3		
POGLUT1	56983	hgsc.bcm.edu	37	3	119207780	119207780	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	g.chr3:119207780C>T	ENST00000295588.4	+	8	827	c.743C>T	c.(742-744)aCc>aTc	p.T248I		NM_152305.2	NP_689518.1	Q8NBL1	PGLT1_HUMAN	protein O-glucosyltransferase 1	248					cardiovascular system development (GO:0072358)|Notch signaling pathway (GO:0007219)|protein O-linked glycosylation (GO:0006493)|regulation of Notch signaling pathway (GO:0008593)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)	glucosyltransferase activity (GO:0046527)|protein xylosyltransferase activity (GO:0030158)|UDP-glucosyltransferase activity (GO:0035251)	p.T248I(1)		autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(7)|ovary(1)|prostate(1)	16						TTAAAGGATACCTTAGGAAAG	0.383																																					p.T248I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C743T	3						.						112.0	101.0	105.0					3																	119207780		2203	4300	6503	120690470	SO:0001583	missense	56983	exon8			BC030614	CCDS2988.1	3q13.33	2010-09-29	2010-09-29	2010-09-29	ENSG00000163389	ENSG00000163389			22954	protein-coding gene	gene with protein product	"""KDELC family like 1"""	615618	"""chromosome 3 open reading frame 9"", ""KTEL (Lys-Tyr-Glu-Leu) containing 1"""	C3orf9, KTELC1		16524674	Standard	NM_152305		Approved	MDS010, MGC32995, 9630046K23Rik, MDSRP, hCLP46, KDELCL1, Rumi	uc003ecm.3	Q8NBL1	OTTHUMG00000159379	ENST00000295588.4:c.743C>T	3.37:g.119207780C>T	ENSP00000295588:p.Thr248Ile	Somatic		Capture	SOLID	Phase_I	120690470	NM_152305	B2RD13|Q53GJ4|Q8N2T1	Missense_Mutation	SNP	ENST00000295588.4	37	CCDS2988.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.738773	0.89573	.	.	ENSG00000163389	ENST00000295588	T	0.23147	1.92	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.46600	0.1401	M	0.65320	2	0.80722	D	1	D	0.76494	0.999	D	0.68353	0.957	T	0.14896	-1.0456	10	0.32370	T	0.25	-11.7006	15.3842	0.74684	0.0:1.0:0.0:0.0	.	248	Q8NBL1	PGLT1_HUMAN	I	248	ENSP00000295588:T248I	ENSP00000295588:T248I	T	+	2	0	POGLUT1	120690470	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	7.464000	0.80887	2.713000	0.92767	0.655000	0.94253	ACC		0.383	POGLUT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355034.2	NM_152305	
RAF1	5894	hgsc.bcm.edu	37	3	12645699	12645699	+	Missense_Mutation	SNP	G	G	A	rs80338796		TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	g.chr3:12645699G>A	ENST00000251849.4	-	7	1209	c.770C>T	c.(769-771)tCg>tTg	p.S257L	RAF1_ENST00000542177.1_Missense_Mutation_p.S176L|RAF1_ENST00000534997.1_Missense_Mutation_p.S42L|RAF1_ENST00000442415.2_Missense_Mutation_p.S257L	NM_002880.3	NP_002871.1	P04049	RAF1_HUMAN	Raf-1 proto-oncogene, serine/threonine kinase	257			S -> L (in NS5 and LEOPARD2; shows in vitro greater kinase activity and enhanced ERK activation than wild-type). {ECO:0000269|PubMed:17603482, ECO:0000269|PubMed:17603483}.		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.S257L(3)|p.S257W(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)	TGTGGATGTCGACCTCTGCCT	0.527			T	SRGAP3	pilocytic astrocytoma				Noonan syndrome																												p.S257L			Dom	yes		3	3p25	5894	v-raf-1 murine leukemia viral oncogene homolog 1		M	.	.	4	Substitution - Missense(4)	large_intestine(3)|lung(1)	c.C770T	3	GRCh37	CM073301	RAF1	M	rs80338796	.						157.0	138.0	145.0					3																	12645699		2203	4300	6503	12620699	SO:0001583	missense	5894	exon7	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	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.770C>T	3.37:g.12645699G>A	ENSP00000251849:p.Ser257Leu	Somatic		Capture	SOLID	Phase_I	12620699	NM_002880	B0LPH8|B2R5N3|Q15278|Q9UC20	Missense_Mutation	SNP	ENST00000251849.4	37	CCDS2612.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.523633	0.85600	.	.	ENSG00000132155	ENST00000251849;ENST00000442415;ENST00000432427;ENST00000534997;ENST00000542177	T;T;T;T;T	0.77358	-1.07;-1.09;-1.01;-0.96;-1.05	5.73	5.73	0.89815	.	0.108329	0.64402	D	0.000003	T	0.81173	0.4767	M	0.81802	2.56	0.80722	A	1	P;P;B	0.48230	0.907;0.746;0.337	B;B;B	0.40741	0.339;0.226;0.117	D	0.85183	0.1005	9	0.87932	D	0	.	20.2602	0.98440	0.0:0.0:1.0:0.0	.	176;42;257	B4E0X2;B4E1N6;P04049	.;.;RAF1_HUMAN	L	257;257;136;42;176	ENSP00000251849:S257L;ENSP00000401888:S257L;ENSP00000398591:S136L;ENSP00000441186:S42L;ENSP00000443567:S176L	ENSP00000251849:S257L	S	-	2	0	RAF1	12620699	1.000000	0.71417	0.974000	0.42286	0.322000	0.28314	9.807000	0.99171	2.861000	0.98227	0.655000	0.94253	TCG		0.527	RAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252015.2	NM_002880	
GSK3B	2932	hgsc.bcm.edu	37	3	119585439	119585439	+	Intron	SNP	G	G	A			TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	g.chr3:119585439G>A	ENST00000264235.8	-	9	1892				GSK3B_ENST00000473886.1_Intron|GSK3B_ENST00000316626.5_Missense_Mutation_p.R316W	NM_001146156.1|NM_002093.3	NP_001139628.1|NP_002084.2	P49841	GSK3B_HUMAN	glycogen synthase kinase 3 beta						axon guidance (GO:0007411)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell migration (GO:0016477)|cellular response to interleukin-3 (GO:0036016)|cellular response to mechanical stimulus (GO:0071260)|circadian rhythm (GO:0007623)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial to mesenchymal transition (GO:0001837)|ER overload response (GO:0006983)|establishment of cell polarity (GO:0030010)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|fat cell differentiation (GO:0045444)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glycogen metabolic process (GO:0005977)|hippocampus development (GO:0021766)|hypermethylation of CpG island (GO:0044027)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|myoblast fusion (GO:0007520)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle hypertrophy (GO:0010614)|negative regulation of dendrite morphogenesis (GO:0050774)|negative regulation of glycogen (starch) synthase activity (GO:2000466)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of neuron maturation (GO:0014043)|negative regulation of neuron projection development (GO:0010977)|negative regulation of NFAT protein import into nucleus (GO:0051534)|negative regulation of protein binding (GO:0032091)|negative regulation of protein complex assembly (GO:0031333)|negative regulation of type B pancreatic cell development (GO:2000077)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901030)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein binding (GO:0032092)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of stem cell differentiation (GO:2000738)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|protein localization to microtubule (GO:0035372)|protein phosphorylation (GO:0006468)|re-entry into mitotic cell cycle (GO:0000320)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of microtubule-based process (GO:0032886)|regulation of neuronal synaptic plasticity (GO:0048168)|response to drug (GO:0042493)|response to lithium ion (GO:0010226)|superior temporal gyrus development (GO:0071109)	beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|growth cone (GO:0030426)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|beta-catenin binding (GO:0008013)|kinase activity (GO:0016301)|NF-kappaB binding (GO:0051059)|p53 binding (GO:0002039)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II transcription factor binding (GO:0001085)|tau-protein kinase activity (GO:0050321)|ubiquitin protein ligase binding (GO:0031625)	p.R316W(2)		endometrium(1)|large_intestine(8)|lung(7)|prostate(2)	18				GBM - Glioblastoma multiforme(114;0.24)	Lithium(DB01356)	GTACATACCCGCACTCCTGAG	0.373																																					p.R316W												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C946T	3						.						95.0	103.0	100.0					3																	119585439		2203	4300	6503	121068129	SO:0001627	intron_variant	2932	exon9			BC012760	CCDS2996.1, CCDS54628.1	3q13.3	2008-02-15			ENSG00000082701	ENSG00000082701			4617	protein-coding gene	gene with protein product		605004				10486203	Standard	NM_002093		Approved		uc003edm.3	P49841	OTTHUMG00000133765	ENST00000264235.8:c.910-2987C>T	3.37:g.119585439G>A		Somatic		Capture	SOLID	Phase_I	121068129	NM_002093	D3DN89|Q9BWH3|Q9UL47	Missense_Mutation	SNP	ENST00000264235.8	37	CCDS54628.1	.	.	.	.	.	.	.	.	.	.	G	15.31	2.794787	0.50102	.	.	ENSG00000082701	ENST00000316626	T	0.61742	0.08	4.37	4.37	0.52481	.	0.000000	0.38217	N	0.001765	T	0.75049	0.3797	.	.	.	0.44579	D	0.997547	D	0.76494	0.999	D	0.69307	0.963	T	0.79629	-0.1724	9	0.87932	D	0	-2.049	15.3554	0.74423	0.0:0.0:1.0:0.0	.	316	P49841-2	.	W	316	ENSP00000324806:R316W	ENSP00000324806:R316W	R	-	1	2	GSK3B	121068129	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.848000	0.69458	2.262000	0.75019	0.558000	0.71614	CGG		0.373	GSK3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258240.2		
CEP63	80254	hgsc.bcm.edu	37	3	134264515	134264515	+	Missense_Mutation	SNP	C	C	T	rs562546768		TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	g.chr3:134264515C>T	ENST00000337090.3	+	7	816	c.643C>T	c.(643-645)Cgg>Tgg	p.R215W	CEP63_ENST00000354446.3_Missense_Mutation_p.R215W|CEP63_ENST00000383229.3_Missense_Mutation_p.R215W|CEP63_ENST00000332047.5_Missense_Mutation_p.R215W|CEP63_ENST00000513612.2_Missense_Mutation_p.R215W|CEP63_ENST00000606977.1_Missense_Mutation_p.R215W			Q96MT8	CEP63_HUMAN	centrosomal protein 63kDa	215					centriole replication (GO:0007099)|DNA damage checkpoint (GO:0000077)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|signal transduction in response to DNA damage (GO:0042770)|spindle assembly (GO:0051225)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|spindle pole (GO:0000922)		p.R215W(1)		kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27						TAAACTGGAGCGGGCTAATGA	0.448													C|||	1	0.000199681	0.0	0.0	5008	,	,		15475	0.0		0.0	False		,,,				2504	0.001				p.R215W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C643T	3						.						102.0	93.0	96.0					3																	134264515		2203	4300	6503	135747205	SO:0001583	missense	80254	exon7			AK056465	CCDS3086.1, CCDS43152.1, CCDS43153.1, CCDS43154.1	3q22.1	2014-02-20			ENSG00000182923	ENSG00000182923			25815	protein-coding gene	gene with protein product		614724				14654843, 24240477	Standard	NM_001042383		Approved	FLJ13386	uc003eqo.1	Q96MT8	OTTHUMG00000159725	ENST00000337090.3:c.643C>T	3.37:g.134264515C>T	ENSP00000336524:p.Arg215Trp	Somatic		Capture	SOLID	Phase_I	135747205	NM_001042383	D3DND8|D3DND9|D3DNE0|Q96CR0|Q9H8F5|Q9H8N0	Missense_Mutation	SNP	ENST00000337090.3	37	CCDS3086.1	.	.	.	.	.	.	.	.	.	.	C	20.1	3.934062	0.73442	.	.	ENSG00000182923	ENST00000332047;ENST00000354446;ENST00000337090;ENST00000383229;ENST00000513612	T;T;T;T;T	0.35048	1.34;1.74;2.02;1.33;2.02	5.88	3.86	0.44501	.	0.200777	0.40818	N	0.001019	T	0.56659	0.2000	M	0.68952	2.095	0.46416	D	0.999034	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.994;0.998;0.997;0.997	T	0.60485	-0.7254	10	0.59425	D	0.04	-14.2818	13.2952	0.60292	0.401:0.599:0.0:0.0	.	215;215;215;215	Q96MT8;Q96MT8-2;Q96MT8-4;Q96MT8-3	CEP63_HUMAN;.;.;.	W	215	ENSP00000328382:R215W;ENSP00000346432:R215W;ENSP00000336524:R215W;ENSP00000372716:R215W;ENSP00000426129:R215W	ENSP00000328382:R215W	R	+	1	2	CEP63	135747205	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	1.196000	0.32198	1.420000	0.47138	0.650000	0.86243	CGG		0.448	CEP63-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000470139.1	NM_025180	
CCDC50	152137	hgsc.bcm.edu	37	3	191107300	191107300	+	Silent	SNP	C	C	A			TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	.			Illumina GAIIx	TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	g.chr3:191107300C>A	ENST00000392455.3	+	10	1408	c.810C>A	c.(808-810)atC>atA	p.I270I	CCDC50_ENST00000392456.3_Silent_p.I446I	NM_174908.3	NP_777568.1	Q8IVM0	CCD50_HUMAN	coiled-coil domain containing 50	270						cytoplasm (GO:0005737)	ubiquitin protein ligase binding (GO:0031625)	p.I446I(1)		endometrium(5)|kidney(1)|large_intestine(4)|lung(12)|stomach(1)	23	all_cancers(143;8.88e-09)|Ovarian(172;0.103)|Breast(254;0.221)		LUSC - Lung squamous cell carcinoma(58;2.42e-06)|Lung(62;2.86e-06)	GBM - Glioblastoma multiforme(46;0.000136)		CACCACCTATCATGACAGATG	0.423																																					p.I270I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C810A	3						.						207.0	203.0	205.0					3																	191107300		2203	4300	6503	192589994	SO:0001819	synonymous_variant	152137	exon10			AJ416916	CCDS33912.1, CCDS33913.1	3q28	2010-12-24		2005-12-23	ENSG00000152492	ENSG00000152492			18111	protein-coding gene	gene with protein product		611051	"""deafness, autosomal dominant 44"""	C3orf6, DFNA44		16803894, 17503326	Standard	NM_178335		Approved	Ymer	uc003fsv.3	Q8IVM0	OTTHUMG00000156177	ENST00000392455.3:c.810C>A	3.37:g.191107300C>A		Somatic		Capture	SOLID	Phase_I	192589994	NM_174908	Q86VH7	Silent	SNP	ENST00000392455.3	37	CCDS33913.1																																																																																				0.423	CCDC50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343315.1	NM_174908	
RERG	85004	hgsc.bcm.edu	37	12	15262420	15262420	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	g.chr12:15262420C>T	ENST00000256953.2	-	5	560	c.224G>A	c.(223-225)cGa>cAa	p.R75Q	RERG_ENST00000536465.1_Missense_Mutation_p.R75Q|RERG_ENST00000538313.1_Missense_Mutation_p.R75Q|RERG_ENST00000546331.1_Missense_Mutation_p.R56Q|RERG-IT1_ENST00000539734.1_RNA	NM_032918.2	NP_116307.1	Q96A58	RERG_HUMAN	RAS-like, estrogen-regulated, growth inhibitor	75					negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|response to hormone (GO:0009725)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	estrogen receptor binding (GO:0030331)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.R75Q(1)		NS(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	16						TTCCCCCCATCGCATGTGCCC	0.463																																					p.R75Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G224A	12						.						271.0	281.0	278.0					12																	15262420		2203	4300	6503	15153687	SO:0001583	missense	85004	exon5			AF339750	CCDS8673.1, CCDS53753.1	12p13.1	2014-05-09			ENSG00000134533	ENSG00000134533			15980	protein-coding gene	gene with protein product		612664				11533059	Standard	NM_032918		Approved	MGC15754	uc001rct.3	Q96A58	OTTHUMG00000168745	ENST00000256953.2:c.224G>A	12.37:g.15262420C>T	ENSP00000256953:p.Arg75Gln	Somatic		Capture	SOLID	Phase_I	15153687	NM_032918	B2R9R0|B4DI02	Missense_Mutation	SNP	ENST00000256953.2	37	CCDS8673.1	.	.	.	.	.	.	.	.	.	.	C	19.80	3.895503	0.72639	.	.	ENSG00000134533	ENST00000256953;ENST00000538313;ENST00000536465;ENST00000546331;ENST00000545567	D;D;D;D;T	0.81821	-1.54;-1.54;-1.54;-1.54;-0.63	5.01	4.1	0.47936	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.85496	0.5710	L	0.60845	1.875	0.80722	D	1	D;D	0.76494	0.993;0.999	P;D	0.65140	0.782;0.932	D	0.86499	0.1802	10	0.87932	D	0	.	11.9046	0.52703	0.0:0.9138:0.0:0.0862	.	56;75	B4DI02;Q96A58	.;RERG_HUMAN	Q	75;75;75;56;88	ENSP00000256953:R75Q;ENSP00000441505:R75Q;ENSP00000438280:R75Q;ENSP00000444485:R56Q;ENSP00000439532:R88Q	ENSP00000256953:R75Q	R	-	2	0	RERG	15153687	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	6.037000	0.70956	2.489000	0.83994	0.655000	0.94253	CGA		0.463	RERG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400882.1	NM_032918	
STAT6	6778	hgsc.bcm.edu	37	12	57499025	57499025	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	g.chr12:57499025C>T	ENST00000300134.3	-	9	1235	c.910G>A	c.(910-912)Gcc>Acc	p.A304T	STAT6_ENST00000454075.3_Missense_Mutation_p.A304T|STAT6_ENST00000556155.1_Missense_Mutation_p.A304T|STAT6_ENST00000537215.2_Missense_Mutation_p.A194T|STAT6_ENST00000538913.2_Missense_Mutation_p.A194T|STAT6_ENST00000543873.2_Missense_Mutation_p.A304T	NM_001178078.1|NM_003153.4	NP_001171549.1|NP_003144.3	P42226	STAT6_HUMAN	signal transducer and activator of transcription 6, interleukin-4 induced	304					cellular response to hydrogen peroxide (GO:0070301)|cellular response to reactive nitrogen species (GO:1902170)|innate immune response (GO:0045087)|interleukin-4-mediated signaling pathway (GO:0035771)|mammary gland epithelial cell proliferation (GO:0033598)|mammary gland morphogenesis (GO:0060443)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of isotype switching to IgE isotypes (GO:0048295)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|T-helper 1 cell lineage commitment (GO:0002296)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane raft (GO:0045121)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|protein phosphatase binding (GO:0019903)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)	p.A304T(1)		breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(2)|lung(8)|ovary(4)|skin(1)	28						TTGGCTGGGGCCCCCAGGAAC	0.632																																					p.A304T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G910A	12						.						39.0	43.0	42.0					12																	57499025		2203	4300	6503	55785292	SO:0001583	missense	6778	exon9			BC005823, BQ028928	CCDS8931.1, CCDS53804.1	12q13	2013-02-14				ENSG00000166888		"""SH2 domain containing"""	11368	protein-coding gene	gene with protein product		601512				9605853, 8085155	Standard	NM_003153		Approved	D12S1644, IL-4-STAT	uc001sna.3	P42226		ENST00000300134.3:c.910G>A	12.37:g.57499025C>T	ENSP00000300134:p.Ala304Thr	Somatic		Capture	SOLID	Phase_I	55785292	NM_001178078	A8K316|B7ZA27|F5GXI9|Q5FBW5|Q71UP4	Missense_Mutation	SNP	ENST00000300134.3	37	CCDS8931.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.34|14.34	2.507454|2.507454	0.44558|0.44558	.|.	.|.	ENSG00000166888|ENSG00000166888	ENST00000300134;ENST00000535201;ENST00000538913;ENST00000543873;ENST00000556155;ENST00000537215;ENST00000454075;ENST00000542721;ENST00000542516|ENST00000553533	D;D;D;D;D;D|D	0.87412|0.87966	-2.25;-2.25;-2.25;-2.25;-2.25;-2.25|-2.32	4.37|4.37	-1.13|-1.13	0.09775|0.09775	STAT transcription factor, DNA-binding, subdomain (1);STAT transcription factor, DNA-binding (1);p53-like transcription factor, DNA-binding (1);|.	0.334638|.	0.26871|.	N|.	0.022079|.	T|T	0.75759|0.75759	0.3893|0.3893	N|N	0.24115|0.24115	0.695|0.695	0.33679|0.33679	D|D	0.611868|0.611868	B;B|.	0.13594|.	0.0;0.008|.	B;B|.	0.16289|.	0.002;0.015|.	T|T	0.68070|0.68070	-0.5506|-0.5506	10|6	0.36615|.	T|.	0.2|.	-4.0521|-4.0521	4.2046|4.2046	0.10483|0.10483	0.1597:0.4079:0.0:0.4324|0.1597:0.4079:0.0:0.4324	.|.	304;304|.	A8K4S9;P42226|.	.;STAT6_HUMAN|.	T|D	304;194;194;304;304;194;304;194;304|4	ENSP00000300134:A304T;ENSP00000445409:A194T;ENSP00000438451:A304T;ENSP00000451742:A304T;ENSP00000444530:A194T;ENSP00000401486:A304T|ENSP00000451546:G4D	ENSP00000300134:A304T|.	A|G	-|-	1|2	0|0	STAT6|STAT6	55785292|55785292	0.000000|0.000000	0.05858|0.05858	0.996000|0.996000	0.52242|0.52242	0.994000|0.994000	0.84299|0.84299	0.003000|0.003000	0.13083|0.13083	-0.076000|-0.076000	0.12775|0.12775	-0.367000|-0.367000	0.07326|0.07326	GCC|GGC		0.632	STAT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412248.3	NM_003153	
RPH3A	22895	hgsc.bcm.edu	37	12	113328800	113328800	+	Silent	SNP	C	C	T			TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	g.chr12:113328800C>T	ENST00000389385.4	+	19	2264	c.1767C>T	c.(1765-1767)ttC>ttT	p.F589F	RPH3A_ENST00000420983.2_Silent_p.F589F|RPH3A_ENST00000549913.2_3'UTR|RPH3A_ENST00000543106.2_Silent_p.F589F|RPH3A_ENST00000551052.1_Silent_p.F585F|RPH3A_ENST00000415485.3_Silent_p.F589F|RPH3A_ENST00000548866.1_Silent_p.F540F|RPH3A_ENST00000447659.2_Silent_p.F540F	NM_001143854.1|NM_014954.3	NP_001137326.1|NP_055769.2	Q9Y2J0	RP3A_HUMAN	rabphilin 3A	589	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				intracellular protein transport (GO:0006886)	cell junction (GO:0030054)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phosphatidylinositol phosphate binding (GO:1901981)|transporter activity (GO:0005215)	p.F585F(1)		breast(1)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(16)|ovary(3)|prostate(4)|skin(6)|urinary_tract(1)	47				BRCA - Breast invasive adenocarcinoma(302;0.00453)		CAGACCCATTCGTCAAGCTGT	0.547																																					p.F585F												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1755T	12						.						85.0	62.0	70.0					12																	113328800		2203	4300	6503	111813183	SO:0001819	synonymous_variant	22895	exon18			AB023202	CCDS31904.1, CCDS44979.1	12q24.13	2014-07-02	2014-07-02		ENSG00000089169	ENSG00000089169		"""Synaptotagmins"""	17056	protein-coding gene	gene with protein product		612159	"""rabphilin 3A homolog (mouse)"""			10231032, 7822236	Standard	NM_014954		Approved	KIAA0985, rabphilin, exophilin-1	uc001ttz.3	Q9Y2J0	OTTHUMG00000169713	ENST00000389385.4:c.1767C>T	12.37:g.113328800C>T		Somatic		Capture	SOLID	Phase_I	111813183	NM_014954	B7Z3C3|Q96AE0	Silent	SNP	ENST00000389385.4	37	CCDS44979.1																																																																																				0.547	RPH3A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405561.1	NM_014954	
CCRN4L	25819	hgsc.bcm.edu	37	4	139966481	139966481	+	Silent	SNP	A	A	G			TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	.			Illumina GAIIx	TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	g.chr4:139966481A>G	ENST00000280614.2	+	3	1342	c.1149A>G	c.(1147-1149)aaA>aaG	p.K383K	ELF2_ENST00000515489.1_Intron	NM_012118.2	NP_036250.2	Q9UK39	NOCT_HUMAN	CCR4 carbon catabolite repression 4-like (S. cerevisiae)	383					circadian regulation of gene expression (GO:0032922)|cytoplasmic mRNA processing body assembly (GO:0033962)|deadenylation-dependent decapping of nuclear-transcribed mRNA (GO:0000290)|mRNA processing (GO:0006397)|mRNA stabilization (GO:0048255)|negative regulation of gene expression (GO:0010629)|negative regulation of osteoblast differentiation (GO:0045668)|positive regulation of fat cell differentiation (GO:0045600)|regulation of circadian rhythm (GO:0042752)|regulation of embryonic development (GO:0045995)|regulation of transcription, DNA-templated (GO:0006355)|response to extracellular stimulus (GO:0009991)|response to lipopolysaccharide (GO:0032496)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	metal ion binding (GO:0046872)|mRNA binding (GO:0003729)|poly(A)-specific ribonuclease activity (GO:0004535)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K383K(1)		kidney(2)|large_intestine(3)|lung(3)|ovary(1)	9	all_hematologic(180;0.162)					GGTATTCTAAACATGCTCTAA	0.498																																					p.K383K	Ovarian(144;566 1842 19130 21379 22209)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1149G	4						.						114.0	109.0	110.0					4																	139966481		2203	4300	6503	140185931	SO:0001819	synonymous_variant	25819	exon3			AF183961	CCDS3743.1	4q31.1	2014-06-18	2001-11-28		ENSG00000151014	ENSG00000151014			14254	protein-coding gene	gene with protein product		608468	"""CCR4-like (carbon catabolite repression 4, S.cerevisiae)"""			10521507	Standard	NM_012118		Approved	CCR4L, Ccr4c	uc003ihl.3	Q9UK39	OTTHUMG00000161271	ENST00000280614.2:c.1149A>G	4.37:g.139966481A>G		Somatic		Capture	SOLID	Phase_I	140185931	NM_012118	D3DNY5|Q14D51|Q9HD93|Q9HD94|Q9HD95	Silent	SNP	ENST00000280614.2	37	CCDS3743.1																																																																																				0.498	CCRN4L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257231.3	NM_012118	
PPM1K	152926	hgsc.bcm.edu	37	4	89199646	89199646	+	Silent	SNP	G	G	A	rs141775336		TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	.			Illumina GAIIx	TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	g.chr4:89199646G>A	ENST00000608933.1	-	2	479	c.90C>T	c.(88-90)gaC>gaT	p.D30D	PPM1K_ENST00000508256.1_Intron|PPM1K_ENST00000315194.4_Silent_p.D30D|PPM1K_ENST00000295908.7_Silent_p.D30D|PPM1K_ENST00000514204.1_Silent_p.D30D|PPM1K_ENST00000506423.1_5'UTR	NM_152542.4	NP_689755.3	Q8N3J5	PPM1K_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1K	30					protein dephosphorylation (GO:0006470)	mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)	p.D30D(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|urinary_tract(1)	13		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000192)		CCCGCCTGTCGTCCTGCAGCA	0.557																																					p.D30D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C90T	4						.	G		2,4404	4.2+/-10.8	0,2,2201	63.0	61.0	62.0		90	-8.6	0.0	4	dbSNP_134	62	0,8600		0,0,4300	no	coding-synonymous	PPM1K	NM_152542.3		0,2,6501	AA,AG,GG		0.0,0.0454,0.0154		30/373	89199646	2,13004	2203	4300	6503	89418670	SO:0001819	synonymous_variant	152926	exon2			BC037552	CCDS3629.1	4q22.1	2012-04-17	2010-03-05		ENSG00000163644	ENSG00000163644	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"""	25415	protein-coding gene	gene with protein product	"""PP2C-type mitochondrial phosphoprotein phosphatase"", ""protein phosphatase 2C kappa"", ""branched-chain &#945;-ketoacid dehydrogenase phosphatase"""	611065	"""protein phosphatase 1K (PP2C domain containing)"""			22291014	Standard	NM_152542		Approved	DKFZp761G058, PP2Ckappa, hPTMP, PP2Cm, BDP	uc003hrm.5	Q8N3J5	OTTHUMG00000130952	ENST00000608933.1:c.90C>T	4.37:g.89199646G>A		Somatic		Capture	SOLID	Phase_I	89418670	NM_152542	B2RAZ1|Q05CT5|Q49AB5|Q4W5E6|Q56AN8|Q8IUZ7|Q8IXG7|Q8ND70|Q96NT4	Silent	SNP	ENST00000608933.1	37	CCDS3629.1																																																																																				0.557	PPM1K-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253553.4	NM_152542	
FGG	2266	hgsc.bcm.edu	37	4	155533266	155533266	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	g.chr4:155533266C>T	ENST00000336098.3	-	3	249	c.211G>A	c.(211-213)Gac>Aac	p.D71N	FGG_ENST00000407946.1_Missense_Mutation_p.D71N|FGG_ENST00000404648.3_Missense_Mutation_p.D71N|FGG_ENST00000405164.1_Missense_Mutation_p.D71N	NM_021870.2	NP_068656.2	P02679	FIBG_HUMAN	fibrinogen gamma chain	71					blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|cellular protein complex assembly (GO:0043623)|extracellular matrix organization (GO:0030198)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of exocytosis (GO:0045921)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of peptide hormone secretion (GO:0090277)|positive regulation of protein secretion (GO:0050714)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of vasoconstriction (GO:0045907)|protein polymerization (GO:0051258)|response to calcium ion (GO:0051592)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|cell cortex (GO:0005938)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)	cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)|receptor binding (GO:0005102)|structural molecule activity (GO:0005198)	p.D71N(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(9)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	27	all_hematologic(180;0.215)	Renal(120;0.0458)			Sucralfate(DB00364)	TGTAAGATGTCTTCCAAAGAC	0.358																																					p.D71N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G211A	4						.						150.0	135.0	140.0					4																	155533266		2203	4300	6503	155752716	SO:0001583	missense	2266	exon3				CCDS3788.1, CCDS47153.1	4q28	2014-09-17			ENSG00000171557	ENSG00000171557		"""Fibrinogen C domain containing"", ""Endogenous ligands"""	3694	protein-coding gene	gene with protein product		134850	"""fibrinogen, gamma polypeptide"""				Standard	NM_000509		Approved		uc003ioj.3	P02679	OTTHUMG00000150329	ENST00000336098.3:c.211G>A	4.37:g.155533266C>T	ENSP00000336829:p.Asp71Asn	Somatic		Capture	SOLID	Phase_I	155752716	NM_021870	A8K057|P04469|P04470|Q53Y18|Q96A14|Q96KJ3|Q9UC62|Q9UC63|Q9UCF3	Missense_Mutation	SNP	ENST00000336098.3	37	CCDS3788.1	.	.	.	.	.	.	.	.	.	.	C	4.366	0.067467	0.08388	.	.	ENSG00000171557	ENST00000404648;ENST00000405164;ENST00000336098;ENST00000407946	T;T;T;T	0.80824	-1.42;-1.42;-1.42;-1.42	6.17	4.43	0.53597	Fibrinogen, alpha/beta/gamma chain, coiled coil domain (2);	0.740337	0.14366	N	0.324099	T	0.66742	0.2820	L	0.38953	1.18	0.24271	N	0.995243	B;B;B;B	0.06786	0.001;0.0;0.0;0.0	B;B;B;B	0.08055	0.003;0.002;0.002;0.001	T	0.50642	-0.8804	10	0.06891	T	0.86	.	6.885	0.24195	0.0:0.5478:0.2575:0.1947	.	71;71;71;71	C9JC84;P02679;C9JEU5;P02679-2	.;FIBG_HUMAN;.;.	N	71	ENSP00000384860:D71N;ENSP00000384101:D71N;ENSP00000336829:D71N;ENSP00000384552:D71N	ENSP00000336829:D71N	D	-	1	0	FGG	155752716	0.069000	0.21087	0.856000	0.33681	0.383000	0.30230	0.053000	0.14184	0.891000	0.36235	0.655000	0.94253	GAC		0.358	FGG-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317581.1	NM_021870	
CDX4	1046	hgsc.bcm.edu	37	X	72667233	72667233	+	Silent	SNP	G	G	A			TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	g.chrX:72667233G>A	ENST00000373514.2	+	1	144	c.144G>A	c.(142-144)ccG>ccA	p.P48P		NM_005193.1	NP_005184.1	O14627	CDX4_HUMAN	caudal type homeobox 4	48					anterior/posterior pattern specification (GO:0009952)|blood vessel development (GO:0001568)|labyrinthine layer development (GO:0060711)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.P48P(1)		endometrium(4)|kidney(1)|large_intestine(1)|lung(11)|skin(1)	18	Renal(35;0.156)					CTGCGGCACCGGCTTTCTCGC	0.652																																					p.P48P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G144A	X						.						44.0	39.0	41.0					X																	72667233		2203	4300	6503	72583958	SO:0001819	synonymous_variant	1046	exon1			AF029879	CCDS14424.1	Xq13.2	2012-03-09	2007-07-09		ENSG00000131264	ENSG00000131264		"""Homeoboxes / ANTP class : HOXL subclass"""	1808	protein-coding gene	gene with protein product		300025	"""caudal type homeo box transcription factor 4"""			7655457	Standard	NM_005193		Approved		uc011mqk.2	O14627	OTTHUMG00000021831	ENST00000373514.2:c.144G>A	X.37:g.72667233G>A		Somatic		Capture	SOLID	Phase_I	72583958	NM_005193	A1A513|Q5JS20	Silent	SNP	ENST00000373514.2	37	CCDS14424.1																																																																																				0.652	CDX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057229.2	NM_005193	
RPS6KA6	27330	hgsc.bcm.edu	37	X	83360833	83360833	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	G	G	A	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	g.chrX:83360833G>A	ENST00000262752.2	-	16	1424	c.1417C>T	c.(1417-1419)Cgc>Tgc	p.R473C	RPS6KA6_ENST00000543399.1_Missense_Mutation_p.R473C|RPS6KA6_ENST00000495332.1_5'UTR	NM_014496.4	NP_055311.1	Q9UK32	KS6A6_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 6	473	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|central nervous system development (GO:0007417)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|negative regulation of embryonic development (GO:0045992)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of mesoderm development (GO:2000381)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.R473C(1)		NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(26)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	46						TGTCCATAGCGCATCAATATT	0.313																																					p.R473C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1417T	X						.						112.0	101.0	104.0					X																	83360833		2203	4293	6496	83247489	SO:0001583	missense	27330	exon16			AF184965	CCDS14451.1	Xq21.1	2011-04-05	2002-08-29		ENSG00000072133	ENSG00000072133			10435	protein-coding gene	gene with protein product		300303	"""ribosomal protein S6 kinase, 90kD, polypeptide 6"""			10644430	Standard	NM_014496		Approved	RSK4	uc004eej.2	Q9UK32	OTTHUMG00000021923	ENST00000262752.2:c.1417C>T	X.37:g.83360833G>A	ENSP00000262752:p.Arg473Cys	Somatic		Capture	SOLID	Phase_I	83247489	NM_014496	B2R854|B7ZL90|Q6FHX2|Q8WX28|Q9H4S6	Missense_Mutation	SNP	ENST00000262752.2	37	CCDS14451.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.182943	0.78677	.	.	ENSG00000072133	ENST00000262752;ENST00000543399	T;T	0.67698	-0.28;-0.28	4.96	4.09	0.47781	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.79639	0.4480	M	0.72624	2.21	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.993;0.998	T	0.81072	-0.1098	10	0.72032	D	0.01	.	12.68	0.56916	0.0828:0.0:0.9172:0.0	.	473;473	B7ZL90;Q9UK32	.;KS6A6_HUMAN	C	473	ENSP00000262752:R473C;ENSP00000440830:R473C	ENSP00000262752:R473C	R	-	1	0	RPS6KA6	83247489	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.758000	0.85224	0.985000	0.38656	0.544000	0.68410	CGC		0.313	RPS6KA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057372.1	NM_014496	
IL1R2	7850	hgsc.bcm.edu	37	2	102626108	102626108	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	g.chr2:102626108C>A	ENST00000332549.3	+	3	381	c.152C>A	c.(151-153)cCc>cAc	p.P51H	IL1R2_ENST00000441002.1_Missense_Mutation_p.P51H|IL1R2_ENST00000393414.2_Missense_Mutation_p.P51H	NM_004633.3	NP_004624.1	P27930	IL1R2_HUMAN	interleukin 1 receptor, type II	51	Ig-like C2-type 1.				cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type II, blocking receptor activity (GO:0004910)	p.P51H(1)		breast(3)|endometrium(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(1)|skin(1)	28						CTGAGGTGCCCCCAGGTGCCC	0.597																																					p.P51H	Pancreas(106;189 1628 2302 5133 12295)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C152A	2						.						131.0	138.0	135.0					2																	102626108		2203	4300	6503	101992540	SO:0001583	missense	7850	exon3			X59770	CCDS2054.1, CCDS58719.1	2q12	2013-01-11			ENSG00000115590	ENSG00000115590		"""Interleukins and interleukin receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5994	protein-coding gene	gene with protein product		147811		IL1RB		10191101, 1833184	Standard	NM_004633		Approved	CD121b	uc002tbm.3	P27930	OTTHUMG00000130695	ENST00000332549.3:c.152C>A	2.37:g.102626108C>A	ENSP00000330959:p.Pro51His	Somatic		Capture	SOLID	Phase_I	101992540	NM_173343	D3DVJ5|Q6LCE6|Q9UE68	Missense_Mutation	SNP	ENST00000332549.3	37	CCDS2054.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.252176	0.80135	.	.	ENSG00000115590	ENST00000332549;ENST00000393414;ENST00000457817;ENST00000441002	T;T;T;T	0.12255	2.7;2.7;2.7;2.7	5.8	5.8	0.92144	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.071313	0.64402	D	0.000014	T	0.44973	0.1319	M	0.87900	2.915	0.49582	D	0.999805	D	0.89917	1.0	D	0.97110	1.0	T	0.47433	-0.9118	10	0.87932	D	0	.	16.9705	0.86297	0.0:1.0:0.0:0.0	.	51	P27930	IL1R2_HUMAN	H	51	ENSP00000330959:P51H;ENSP00000377066:P51H;ENSP00000408415:P51H;ENSP00000414611:P51H	ENSP00000330959:P51H	P	+	2	0	IL1R2	101992540	0.996000	0.38824	0.998000	0.56505	0.811000	0.45836	4.359000	0.59449	2.758000	0.94735	0.561000	0.74099	CCC		0.597	IL1R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253191.1	NM_004633	
OTOF	9381	hgsc.bcm.edu	37	2	26683819	26683819	+	Silent	SNP	C	C	A			TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	.			Illumina GAIIx	TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	g.chr2:26683819C>A	ENST00000272371.2	-	44	5739	c.5613G>T	c.(5611-5613)ggG>ggT	p.G1871G	OTOF_ENST00000402415.3_Silent_p.G1181G|OTOF_ENST00000338581.6_Silent_p.G1104G|OTOF_ENST00000403946.3_Silent_p.G1871G|OTOF_ENST00000339598.3_Silent_p.G1104G	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN	otoferlin	1871					membrane fusion (GO:0061025)|sensory perception of sound (GO:0007605)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	calcium ion binding (GO:0005509)	p.G1871G(1)|p.G1104G(1)		NS(1)|autonomic_ganglia(1)|breast(9)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(35)|ovary(8)|pancreas(1)|prostate(5)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	106	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CGTCCACCTCCCCGGTGGCCA	0.627																																					p.G1104G	GBM(102;732 1451 20652 24062 31372)											.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G3312T	2						.						74.0	61.0	65.0					2																	26683819		2203	4300	6503	26537323	SO:0001819	synonymous_variant	9381	exon27			AF107403	CCDS1724.1, CCDS1725.1, CCDS1726.1, CCDS46241.1, CCDS74497.1	2p23.1	2014-06-27			ENSG00000115155	ENSG00000115155			8515	protein-coding gene	gene with protein product	"""fer-1-like family member 2"""	603681		DFNB9		10192385, 18381613	Standard	NM_194248		Approved	FER1L2, DFNB6	uc002rhk.3	Q9HC10	OTTHUMG00000096977	ENST00000272371.2:c.5613G>T	2.37:g.26683819C>A		Somatic		Capture	SOLID	Phase_I	26537323	NM_194323	B4DJX0|B5MCC1|B9A0H6|Q53R90|Q9HC08|Q9HC09|Q9Y650	Silent	SNP	ENST00000272371.2	37	CCDS1725.1																																																																																				0.627	OTOF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214047.3		
ALK	238	hgsc.bcm.edu	37	2	29498049	29498049	+	Nonsense_Mutation	SNP	T	T	A			TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	g.chr2:29498049T>A	ENST00000389048.3	-	11	2863	c.1957A>T	c.(1957-1959)Aga>Tga	p.R653*	ALK_ENST00000431873.1_Intron	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	653					activation of MAPK activity (GO:0000187)|cell proliferation (GO:0008283)|neuron development (GO:0048666)|NIK/NF-kappaB signaling (GO:0038061)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|protein complex (GO:0043234)	ATP binding (GO:0005524)|NF-kappaB-inducing kinase activity (GO:0004704)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.R653*(1)	ATIC/ALK(24)|FN1/ALK(2)|C2orf44/ALK(2)|TPM3/ALK(33)|KLC1/ALK(2)|VCL/ALK(4)|TPM4/ALK(12)|KIF5B/ALK(8)|RANBP2/ALK(34)|SQSTM1/ALK(2)|EML4/ALK(543)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|NPM1/ALK(632)|CLTC/ALK(44)|CARS/ALK(5)|MSN/ALK(6)|TFG/ALK(9)	NS(2)|autonomic_ganglia(198)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(4)|large_intestine(25)|lung(61)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|soft_tissue(3)|stomach(2)|thyroid(2)	340	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)|Crizotinib(DB08865)	AACAGGTTTCTTGATTTGGGT	0.498			"""T, Mis, A"""	"""NPM1, TPM3, TFG, TPM4, ATIC, CLTC, MSN, ALO17, CARS, EML4, KIF5B, C2orf22"""	"""ALCL, NSCLC, Neuroblastoma"""	neuroblastoma			Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome																												p.R653X		yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"""L, E, M"""	.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.A1957T	2						.						97.0	98.0	97.0					2																	29498049		2203	4300	6503	29351553	SO:0001587	stop_gained	238	exon11	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	D45915	CCDS33172.1	2p23	2014-09-17	2008-01-23		ENSG00000171094	ENSG00000171094		"""CD molecules"""	427	protein-coding gene	gene with protein product		105590	"""anaplastic lymphoma kinase (Ki-1)"""			8122112	Standard	NM_004304		Approved	CD246	uc002rmy.3	Q9UM73	OTTHUMG00000152034	ENST00000389048.3:c.1957A>T	2.37:g.29498049T>A	ENSP00000373700:p.Arg653*	Somatic		Capture	SOLID	Phase_I	29351553	NM_004304	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Nonsense_Mutation	SNP	ENST00000389048.3	37	CCDS33172.1	.	.	.	.	.	.	.	.	.	.	T	48	14.272988	0.99788	.	.	ENSG00000171094	ENST00000389048	.	.	.	5.21	5.21	0.72293	.	0.117336	0.37437	U	0.002099	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.5095	0.50486	0.0:0.0:0.0:1.0	.	.	.	.	X	653	.	.	R	-	1	2	ALK	29351553	1.000000	0.71417	0.996000	0.52242	0.979000	0.70002	1.457000	0.35212	1.972000	0.57404	0.459000	0.35465	AGA		0.498	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304	
TTN	7273	hgsc.bcm.edu	37	2	179636164	179636164	+	Silent	SNP	G	G	A	rs144247127		TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	.			Illumina GAIIx	TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	g.chr2:179636164G>A	ENST00000591111.1	-	34	8114	c.7890C>T	c.(7888-7890)acC>acT	p.T2630T	TTN_ENST00000360870.5_Silent_p.T2630T|TTN_ENST00000460472.2_Silent_p.T2584T|TTN_ENST00000359218.5_Silent_p.T2584T|TTN_ENST00000342175.6_Silent_p.T2584T|TTN_ENST00000589042.1_Silent_p.T2630T|TTN-AS1_ENST00000610005.1_RNA|TTN_ENST00000342992.6_Silent_p.T2630T|TTN-AS1_ENST00000584485.1_RNA|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12955	Ig-like 15.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.T2584T(3)|p.T2630T(2)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ATTCAGCTACGGTCTGATCTG	0.458																																					p.T2630T												.	.	5	Substitution - coding silent(5)	large_intestine(5)	c.C7890T	2						.	G	,,,,	0,4406		0,0,2203	121.0	104.0	109.0		7752,7890,7890,7752,7752	-12.3	0.1	2	dbSNP_134	109	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	,,,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,,,	2584/26927,2630/33424,2630/5605,2584/27052,2584/27119	179636164	1,13005	2203	4300	6503	179344409	SO:0001819	synonymous_variant	7273	exon34			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.7890C>T	2.37:g.179636164G>A		Somatic		Capture	SOLID	Phase_I	179344409	NM_133379	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																					0.458	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
BRCA2	675	hgsc.bcm.edu	37	13	32931964	32931964	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	.			Illumina GAIIx	TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	g.chr13:32931964T>G	ENST00000380152.3	+	16	7936	c.7703T>G	c.(7702-7704)tTt>tGt	p.F2568C	BRCA2_ENST00000544455.1_Missense_Mutation_p.F2568C			P51587	BRCA2_HUMAN	breast cancer 2, early onset	2568					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.F2568C(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)		GAAGATTATTTTGGTAAGGAA	0.358			"""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)																											p.F2568C	Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"""L, E"""	.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T7703G	13						.						108.0	111.0	110.0					13																	32931964		2203	4300	6503	31829964	SO:0001583	missense	675	exon16	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)	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.7703T>G	13.37:g.32931964T>G	ENSP00000369497:p.Phe2568Cys	Somatic		Capture	SOLID	Phase_I	31829964	NM_000059	O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	37	CCDS9344.1	.	.	.	.	.	.	.	.	.	.	T	18.66	3.672212	0.67928	.	.	ENSG00000139618	ENST00000380152;ENST00000544455	D;D	0.86956	-2.19;-2.19	5.15	3.95	0.45737	DNA recombination/repair protein BRCA2, helical domain (2);	0.118065	0.64402	D	0.000017	D	0.91868	0.7426	M	0.71581	2.175	0.48341	D	0.999633	D	0.89917	1.0	D	0.81914	0.995	D	0.91576	0.5275	10	0.87932	D	0	.	11.2447	0.48990	0.1373:0.0:0.0:0.8627	.	2568	P51587	BRCA2_HUMAN	C	2568	ENSP00000369497:F2568C;ENSP00000439902:F2568C	ENSP00000369497:F2568C	F	+	2	0	BRCA2	31829964	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	7.474000	0.81024	0.780000	0.33566	0.482000	0.46254	TTT		0.358	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059	
FARP1	10160	hgsc.bcm.edu	37	13	99030080	99030080	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	g.chr13:99030080T>G	ENST00000319562.6	+	6	669	c.404T>G	c.(403-405)cTg>cGg	p.L135R	FARP1_ENST00000376586.2_Missense_Mutation_p.L135R|FARP1_ENST00000595437.1_Missense_Mutation_p.L135R	NM_005766.2	NP_005757.1	Q9Y4F1	FARP1_HUMAN	FERM, RhoGEF (ARHGEF) and pleckstrin domain protein 1 (chondrocyte-derived)	135	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				dendrite morphogenesis (GO:0048813)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|synapse assembly (GO:0007416)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|synapse (GO:0045202)	Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.L135R(1)		breast(3)|endometrium(6)|kidney(6)|large_intestine(13)|lung(16)|ovary(1)|skin(3)|urinary_tract(1)	49	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)			CGCAGGTACCTGTTCGCGCTG	0.552																																					p.L135R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T404G	13						.						132.0	111.0	118.0					13																	99030080		2203	4300	6503	97828081	SO:0001583	missense	10160	exon6			AB008430	CCDS9487.1, CCDS32000.1, CCDS66572.1	13q32.2	2013-01-10			ENSG00000152767	ENSG00000152767		"""Rho guanine nucleotide exchange factors"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Pleckstrin homology (PH) domain containing"""	3591	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 75"""	602654				9425278	Standard	NM_005766		Approved	CDEP, PLEKHC2, MGC87400, PPP1R75	uc001vnj.3	Q9Y4F1	OTTHUMG00000017248	ENST00000319562.6:c.404T>G	13.37:g.99030080T>G	ENSP00000322926:p.Leu135Arg	Somatic		Capture	SOLID	Phase_I	97828081	NM_005766	Q5JVI9|Q6IQ29	Missense_Mutation	SNP	ENST00000319562.6	37	CCDS9487.1	.	.	.	.	.	.	.	.	.	.	T	27.1	4.801703	0.90538	.	.	ENSG00000152767	ENST00000376586;ENST00000319562	T;T	0.80480	-1.38;-1.38	5.54	5.54	0.83059	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);	0.000000	0.64402	D	0.000001	D	0.92974	0.7764	H	0.96111	3.77	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.95101	0.8230	10	0.87932	D	0	.	15.6939	0.77477	0.0:0.0:0.0:1.0	.	135;135	Q9Y4F1;C9JME2	FARP1_HUMAN;.	R	135	ENSP00000365771:L135R;ENSP00000322926:L135R	ENSP00000322926:L135R	L	+	2	0	FARP1	97828081	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.673000	0.83973	2.101000	0.63845	0.528000	0.53228	CTG		0.552	FARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045541.3	NM_005766	
PCCA	5095	hgsc.bcm.edu	37	13	101077896	101077896	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	g.chr13:101077896G>A	ENST00000376285.1	+	20	1794	c.1756G>A	c.(1756-1758)Gat>Aat	p.D586N	PCCA_ENST00000376279.3_Missense_Mutation_p.D586N|PCCA_ENST00000376286.4_Missense_Mutation_p.D560N	NM_000282.3	NP_000273.2	P05165	PCCA_HUMAN	propionyl CoA carboxylase, alpha polypeptide	586					biotin metabolic process (GO:0006768)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|propionyl-CoA carboxylase activity (GO:0004658)	p.D586N(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(12)|lung(8)|prostate(1)|skin(2)	26	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Biotin(DB00121)	GGTGGAAGTTGATGGGTCGAA	0.458																																					p.D586N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1756A	13						.						170.0	140.0	150.0					13																	101077896		2203	4300	6503	99875897	SO:0001583	missense	5095	exon20			X14608	CCDS9496.2, CCDS45065.1, CCDS53878.1	13q32	2011-01-14	2010-04-30		ENSG00000175198	ENSG00000175198	6.4.1.3		8653	protein-coding gene	gene with protein product		232000	"""propionyl Coenzyme A carboxylase, alpha polypeptide"""			1427880	Standard	NM_000282		Approved		uc001voo.3	P05165	OTTHUMG00000017284	ENST00000376285.1:c.1756G>A	13.37:g.101077896G>A	ENSP00000365462:p.Asp586Asn	Somatic		Capture	SOLID	Phase_I	99875897	NM_001178004	B4DKY8|B4DPF9|C9JPQ8|Q15979|Q8WXQ7	Missense_Mutation	SNP	ENST00000376285.1	37	CCDS9496.2	.	.	.	.	.	.	.	.	.	.	G	25.0	4.588377	0.86851	.	.	ENSG00000175198	ENST00000376286;ENST00000376279;ENST00000376285;ENST00000424527;ENST00000536640	D;D;D;D	0.82526	-1.62;-1.62;-1.62;-1.62	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.81758	0.4890	L	0.50333	1.59	0.80722	D	1	B;B;B	0.21606	0.058;0.024;0.058	B;B;B	0.26969	0.034;0.075;0.056	T	0.75994	-0.3121	10	0.37606	T	0.19	.	19.8351	0.96655	0.0:0.0:1.0:0.0	.	586;560;586	C9JPQ8;P05165-2;P05165	.;.;PCCA_HUMAN	N	560;586;586;120;82	ENSP00000365463:D560N;ENSP00000365456:D586N;ENSP00000365462:D586N;ENSP00000396050:D120N	ENSP00000365456:D586N	D	+	1	0	PCCA	99875897	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.621000	0.90949	2.693000	0.91896	0.650000	0.86243	GAT		0.458	PCCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045627.2		
GRID1	2894	hgsc.bcm.edu	37	10	87966374	87966374	+	Silent	SNP	G	G	A			TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	.			Illumina GAIIx	TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	g.chr10:87966374G>A	ENST00000327946.7	-	3	352	c.267C>T	c.(265-267)gcC>gcT	p.A89A		NM_017551.2	NP_060021.1	Q9ULK0	GRID1_HUMAN	glutamate receptor, ionotropic, delta 1	89					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|social behavior (GO:0035176)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|ionotropic glutamate receptor complex (GO:0008328)|postsynaptic membrane (GO:0045211)	extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)	p.A89A(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(46)|ovary(5)|prostate(4)|skin(5)|stomach(4)|upper_aerodigestive_tract(5)	106						ACGTGACCAAGGCCAAAATCC	0.587										Multiple Myeloma(13;0.14)																											p.A89A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C267T	10						.						82.0	55.0	65.0					10																	87966374		2203	4300	6503	87956354	SO:0001819	synonymous_variant	2894	exon3			AB033046	CCDS31236.1	10q22	2012-08-29			ENSG00000182771	ENSG00000182771		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4575	protein-coding gene	gene with protein product		610659					Standard	NM_017551		Approved	GluD1, KIAA1220	uc001kdl.1	Q9ULK0	OTTHUMG00000018650	ENST00000327946.7:c.267C>T	10.37:g.87966374G>A		Somatic		Capture	SOLID	Phase_I	87956354	NM_017551	B3KXD5|B7Z7L0|Q8IXT3	Silent	SNP	ENST00000327946.7	37	CCDS31236.1																																																																																				0.587	GRID1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049148.3	XM_043613	
APC	324	hgsc.bcm.edu	37	5	112162891	112162891	+	Nonsense_Mutation	SNP	C	C	T	rs137854580		TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	g.chr5:112162891C>T	ENST00000457016.1	+	12	1875	c.1495C>T	c.(1495-1497)Cga>Tga	p.R499*	APC_ENST00000257430.4_Nonsense_Mutation_p.R499*|APC_ENST00000508376.2_Nonsense_Mutation_p.R499*|CTC-554D6.1_ENST00000520401.1_5'Flank			P25054	APC_HUMAN	adenomatous polyposis coli	499	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R499*(5)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TACACTAAGACGATATGCTGG	0.373		12	"""D, Mis, N, F, S"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											p.R481X	NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	APC,large_intestine,colon,Substitution - Nonsense,0	.	6	Substitution - Nonsense(5)|Unknown(1)	large_intestine(5)|skin(1)	c.C1441T	5	GRCh37	CM930023	APC	M	rs137854580	.						135.0	123.0	127.0					5																	112162891		2202	4300	6502	112190790	SO:0001587	stop_gained	324	exon10	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.1495C>T	5.37:g.112162891C>T	ENSP00000413133:p.Arg499*	Somatic		Capture	SOLID	Phase_I	112190790	NM_001127511	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	40	8.025077	0.98616	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.85	4.98	0.66077	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.3767	14.9298	0.70906	0.2732:0.7267:0.0:0.0	.	.	.	.	X	499;481;499;499;499	.	ENSP00000257430:R499X	R	+	1	2	APC	112190790	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.513000	0.35823	1.461000	0.47929	0.655000	0.94253	CGA		0.373	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
ADAMTS12	81792	hgsc.bcm.edu	37	5	33549337	33549337	+	Missense_Mutation	SNP	G	G	A	rs144560370		TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	g.chr5:33549337G>A	ENST00000504830.1	-	21	4612	c.4277C>T	c.(4276-4278)gCg>gTg	p.A1426V	ADAMTS12_ENST00000352040.3_Missense_Mutation_p.A1341V	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	1426	TSP type-1 7. {ECO:0000255|PROSITE- ProRule:PRU00210}.				cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of cellular response to hepatocyte growth factor stimulus (GO:2001113)|negative regulation of cellular response to vascular endothelial growth factor stimulus (GO:1902548)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of hepatocyte growth factor receptor signaling pathway (GO:1902203)|proteoglycan catabolic process (GO:0030167)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of endothelial tube morphogenesis (GO:1901509)|regulation of inflammatory response (GO:0050727)	extracellular matrix (GO:0031012)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.A1426V(1)		NS(1)|breast(7)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(31)|liver(1)|lung(135)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	216						CACCTGCCACGCCTCACAGGG	0.592										HNSCC(64;0.19)			G|||	1	0.000199681	0.0	0.0	5008	,	,		18276	0.001		0.0	False		,,,				2504	0.0				p.A1426V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C4277T	5						.						54.0	52.0	53.0					5																	33549337		2203	4300	6503	33585094	SO:0001583	missense	81792	exon21			AJ250725	CCDS34140.1	5q35	2008-07-18	2005-08-19		ENSG00000151388	ENSG00000151388		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	14605	protein-coding gene	gene with protein product		606184	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 12"""			11279086	Standard	NM_030955		Approved		uc003jia.1	P58397	OTTHUMG00000162088	ENST00000504830.1:c.4277C>T	5.37:g.33549337G>A	ENSP00000422554:p.Ala1426Val	Somatic		Capture	SOLID	Phase_I	33585094	NM_030955	A2RRN9|A5D6V6|Q6UWL3	Missense_Mutation	SNP	ENST00000504830.1	37	CCDS34140.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	10.96	1.498769	0.26861	.	.	ENSG00000151388	ENST00000504830;ENST00000352040	T;T	0.59638	0.25;0.25	5.37	1.46	0.22682	.	0.726152	0.14053	N	0.344581	T	0.31796	0.0808	N	0.11284	0.12	0.80722	D	1	B;B	0.30482	0.281;0.012	B;B	0.24006	0.05;0.001	T	0.03706	-1.1011	10	0.33141	T	0.24	.	6.9967	0.24786	0.1397:0.0:0.2946:0.5657	.	1341;1426	P58397-3;P58397	.;ATS12_HUMAN	V	1426;1341	ENSP00000422554:A1426V;ENSP00000344847:A1341V	ENSP00000344847:A1341V	A	-	2	0	ADAMTS12	33585094	0.977000	0.34250	0.878000	0.34440	0.576000	0.36127	1.807000	0.38902	0.027000	0.15297	-1.179000	0.01719	GCG		0.592	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	NM_030955	
TCOF1	6949	hgsc.bcm.edu	37	5	149749131	149749131	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3562-01A-02W-0831-10	TCGA-AA-3562-10A-01W-0831-10	g.chr5:149749131A>G	ENST00000504761.2	+	6	605	c.605A>G	c.(604-606)gAc>gGc	p.D202G	TCOF1_ENST00000513346.1_Missense_Mutation_p.D202G|TCOF1_ENST00000439160.2_Missense_Mutation_p.D202G|TCOF1_ENST00000394269.3_Missense_Mutation_p.D202G|TCOF1_ENST00000451292.1_Missense_Mutation_p.D202G|TCOF1_ENST00000323668.7_Missense_Mutation_p.D202G|TCOF1_ENST00000377797.3_Missense_Mutation_p.D202G|TCOF1_ENST00000445265.2_Missense_Mutation_p.D202G			Q13428	TCOF_HUMAN	Treacher Collins-Franceschetti syndrome 1	202					skeletal system development (GO:0001501)|transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:0042790)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transporter activity (GO:0005215)	p.D202G(1)		NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(8)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	35		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TCCAGCGAGGACACCTCCAGC	0.632																																					p.D202G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A605G	5						.						89.0	79.0	82.0					5																	149749131		2203	4300	6503	149729324	SO:0001583	missense	6949	exon6				CCDS4306.1, CCDS47305.1, CCDS47306.1, CCDS47307.1, CCDS54936.1	5q32	2014-06-18			ENSG00000070814	ENSG00000070814			11654	protein-coding gene	gene with protein product		606847				1765376	Standard	NM_001008657		Approved	treacle, TCS	uc003lry.3	Q13428	OTTHUMG00000130081	ENST00000504761.2:c.605A>G	5.37:g.149749131A>G	ENSP00000421655:p.Asp202Gly	Somatic		Capture	SOLID	Phase_I	149729324	NM_001135243	A0JLU0|B4E111|Q6SC72|Q7Z5W9|Q96A52|Q99408|Q99860	Missense_Mutation	SNP	ENST00000504761.2	37	CCDS54936.1	.	.	.	.	.	.	.	.	.	.	A	17.84	3.487226	0.63962	.	.	ENSG00000070814	ENST00000451292;ENST00000377797;ENST00000445265;ENST00000323668;ENST00000439160;ENST00000394269;ENST00000427724;ENST00000504761;ENST00000513346	T;T;T;T;T;T;T;T;T	0.79352	-1.12;-1.14;-1.25;-1.26;-1.12;1.24;-1.12;-1.13;-1.12	4.05	4.05	0.47172	.	0.000000	0.40385	N	0.001107	T	0.79015	0.4375	L	0.32530	0.975	0.24078	N	0.99595	D;D;D;D;D;D	0.76494	0.998;0.989;0.998;0.999;0.989;0.996	D;P;D;D;P;P	0.66084	0.941;0.846;0.941;0.94;0.846;0.846	T	0.69000	-0.5261	10	0.59425	D	0.04	-13.3936	9.6925	0.40136	1.0:0.0:0.0:0.0	.	202;202;202;202;202;202	Q13428-7;Q13428-2;Q13428-6;Q13428;Q13428-8;Q13428-5	.;.;.;TCOF_HUMAN;.;.	G	202	ENSP00000400939:D202G;ENSP00000367028:D202G;ENSP00000409944:D202G;ENSP00000325223:D202G;ENSP00000406888:D202G;ENSP00000377811:D202G;ENSP00000390717:D202G;ENSP00000421655:D202G;ENSP00000427484:D202G	ENSP00000325223:D202G	D	+	2	0	TCOF1	149729324	0.998000	0.40836	0.990000	0.47175	0.851000	0.48451	3.612000	0.54142	2.063000	0.61619	0.379000	0.24179	GAC		0.632	TCOF1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380552.1	NM_001008656	
