#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_Annotation_Transcript	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Mutation_Type	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Other_Diseases	i_CGC_Tissue Type	i_CGC_Translocation_Partner	i_CGC_Tumor_Types_Germline	i_CGC_Tumor_Types_Somatic	i_COSMIC_fusion_genes	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_mutations	i_COSMIC_overlapping_primary_sites	i_COSMIC_tissue_types_affected	i_COSMIC_total_alterations_in_gene	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Codon_Change	i_DNARepairGenes_Role	i_Description	i_DrugBank	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_FamilialCancerDatabase_Syndromes	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GO_Biological_Process	i_GO_Cellular_Component	i_GO_Molecular_Function	i_Genome_Change	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_MUTSIG_Published_Results	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_SwissProt_acc_Id	i_SwissProt_entry_Id	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	i_Transcript_Exon	i_Transcript_Position	i_Transcript_Strand	i_Tumorscape_Amplification_Peaks	i_Tumorscape_Deletion_Peaks	i_UniProt_AApos	i_UniProt_Experimental_Info	i_UniProt_Natural_Variations	i_UniProt_Region	i_UniProt_Site	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_cDNA_Change	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_ref_count_full	isArtifactMode	oxoGCut	pox	pox_cutoff	qox	t_alt_count	t_ref_count	validation_alt_allele	validation_method	validation_status	validation_tumor_sample
GPATCH8	23131	broad.mit.edu	37	17	42475015	42475015	+	Missense_Mutation	SNP	G	G	C			TCGA-EL-A3CZ-01A-11D-A19J-08	TCGA-EL-A3CZ-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	25c1a1a4-82e1-485a-afce-cafaed57945f	15fb2f33-0687-4679-b3b1-2244f979c0a7	g.chr17:42475015G>C	ENST00000591680.1	-	8	4460	c.4430C>G	c.(4429-4431)aCt>aGt	p.T1477S	GPATCH8_ENST00000434000.1_Missense_Mutation_p.T1399S	NM_001002909.2	NP_001002909.1	Q9UKJ3	GPTC8_HUMAN	G patch domain containing 8	1477	Poly-Ala.						metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.A1474_A1478delAAATA(1)		breast(4)|endometrium(7)|kidney(6)|large_intestine(4)|liver(2)|lung(21)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	50		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.206)		GTGAAGTGCAGTGGCAGCTGC	0.612																																						ENST00000434000.1																			1	Deletion - In frame(1)	p.A1474_A1478delAAATA(1)	liver(1)	breast(4)|endometrium(7)|kidney(6)|large_intestine(4)|liver(2)|lung(21)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	50						c.(4195-4197)aCt>aGt		G patch domain containing 8							72.0	63.0	66.0					17																	42475015		2203	4300	6503	SO:0001583	missense	23131					intracellular	nucleic acid binding|zinc ion binding	g.chr17:42475015G>C	AB011125	CCDS32666.1	17q21.31	2013-01-28	2006-08-22	2006-12-13	ENSG00000186566	ENSG00000186566		"""G patch domain containing"""	29066	protein-coding gene	gene with protein product		614396	"""KIAA0553"""	KIAA0553, GPATC8		9628581	Standard	NM_001002909		Approved		uc002igw.2	Q9UKJ3	OTTHUMG00000181818	ENST00000591680.1:c.4430C>G	17.37:g.42475015G>C	ENSP00000467556:p.Thr1477Ser					GPATCH8_ENST00000591680.1_Missense_Mutation_p.T1477S	p.T1399S			Q9UKJ3	GPTC8_HUMAN		BRCA - Breast invasive adenocarcinoma(366;0.206)	9	4478	-		Prostate(33;0.0181)	1477					B9EGP9|O60300|Q8TB99	Missense_Mutation	SNP	ENST00000591680.1	37	c.4196C>G	CCDS32666.1	.	.	.	.	.	.	.	.	.	.	G	11.94	1.788451	0.31685	.	.	ENSG00000186566	ENST00000335500;ENST00000434000	T	0.10005	2.92	5.34	4.36	0.52297	.	0.203375	0.41938	D	0.000799	T	0.04724	0.0128	N	0.04090	-0.28	0.38992	D	0.959166	B	0.31383	0.321	B	0.23852	0.049	T	0.46400	-0.9194	10	0.15952	T	0.53	-14.1487	13.3988	0.60870	0.0772:0.0:0.9228:0.0	.	1477	Q9UKJ3	GPTC8_HUMAN	S	1477;1399	ENSP00000395016:T1399S	ENSP00000335486:T1477S	T	-	2	0	GPATCH8	39830541	1.000000	0.71417	0.997000	0.53966	0.690000	0.40134	9.394000	0.97261	1.254000	0.44035	0.313000	0.20887	ACT		0.612	GPATCH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457797.1	NM_001002909		9	20	0	0	0	0.004482	0	9	20				
WASH6P	653440	broad.mit.edu	37	X	155254735	155254735	+	RNA	SNP	C	C	G			TCGA-EL-A3CZ-01A-11D-A19J-08	TCGA-EL-A3CZ-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	25c1a1a4-82e1-485a-afce-cafaed57945f	15fb2f33-0687-4679-b3b1-2244f979c0a7	g.chrX:155254735C>G	ENST00000461007.1	+	0	3651				AJ271736.10_ENST00000285718.7_RNA			Q9NQA3	WASH6_HUMAN	WAS protein family homolog 6 pseudogene						Arp2/3 complex-mediated actin nucleation (GO:0034314)|endosomal transport (GO:0016197)|retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|membrane (GO:0016020)|recycling endosome (GO:0055037)|WASH complex (GO:0071203)	alpha-tubulin binding (GO:0043014)	p.L425V(1)									GATGTCGGATCTCTTCAACAA	0.587																																						ENST00000285718.7																			1	Substitution - Missense(1)	p.L425V(1)	kidney(1)																																																0							g.chrX:155254735C>G	AI042587		Xq28 and Yq12	2014-08-28	2008-01-16	2008-01-16	ENSG00000182484	ENSG00000182484		"""Pseudoautosomal regions / PAR2"", ""WAS protein homologs"""	31685	pseudogene	pseudogene			"""family with sequence similarity 39, member A"", ""chromosomes X and Y open reading frame 1"""	FAM39A, CXYorf1		10655549, 12566406, 18159949	Standard	NG_008380		Approved			Q9NQA3	OTTHUMG00000022677		X.37:g.155254735C>G						WASH6P_ENST00000461007.1_RNA								0	1180	+								A6NGF1|Q8N305	RNA	SNP	ENST00000461007.1	37			.	.	.	.	.	.	.	.	.	.	c	15.33	2.802731	0.50315	.	.	ENSG00000182484	ENST00000359512;ENST00000285718	.	.	.	0.379	0.379	0.16213	.	0.186044	0.48286	D	0.000191	T	0.39200	0.1069	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.29822	-0.9999	6	0.72032	D	0.01	-24.1796	6.473	0.22020	0.0:0.9998:0.0:2.0E-4	.	.	.	.	V	425;394	.	ENSP00000285718:L394V	L	+	1	0	WASH6P	154907929	1.000000	0.71417	0.841000	0.33234	0.284000	0.27059	4.956000	0.63645	0.418000	0.25898	0.171000	0.16805	CTC		0.587	WASH6P-016	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000058840.1	NG_008380		5	8	0	0	0	0.001168	0	5	8				
RRN3P2	653390	broad.mit.edu	37	16	29110458	29110458	+	RNA	SNP	T	T	C	rs561841139		TCGA-EL-A3CZ-01A-11D-A19J-08	TCGA-EL-A3CZ-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	25c1a1a4-82e1-485a-afce-cafaed57945f	15fb2f33-0687-4679-b3b1-2244f979c0a7	g.chr16:29110458T>C	ENST00000564580.1	+	0	1131							A6NIE6	RN3P2_HUMAN	RNA polymerase I transcription factor homolog (S. cerevisiae) pseudogene 2									p.W375R(25)									GAATTTTGAGTGGATAGTGAT	0.328																																						ENST00000564580.1																			25	Substitution - Missense(25)	p.W375R(25)	endometrium(19)|kidney(4)|prostate(2)																																																0							g.chr16:29110458T>C			16p11.2	2011-12-02			ENSG00000103472	ENSG00000103472			37619	pseudogene	pseudogene							Standard	NR_003369		Approved		uc002dsf.4	A6NIE6			16.37:g.29110458T>C														0	1131	+									RNA	SNP	ENST00000564580.1	37			.	.	.	.	.	.	.	.	.	.	N	5.632	0.301362	0.10678	.	.	ENSG00000103472	ENST00000427965	.	.	.	1.93	1.93	0.25924	.	0.000000	0.64402	N	0.000001	T	0.11239	0.0274	.	.	.	.	.	.	.	.	.	.	.	.	T	0.29701	-1.0003	5	0.02654	T	1	.	2.7527	0.05285	0.2724:0.5536:0.0:0.174	.	.	.	.	R	375	.	ENSP00000398611:W375R	W	+	1	0	AC009093.1	29017959	1.000000	0.71417	0.564000	0.28396	0.423000	0.31445	3.439000	0.52878	0.163000	0.19507	-1.160000	0.01791	TGG		0.328	RRN3P2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000433243.1	NR_003369		4	47	0	0	0	0.014758	0	4	47				
HRAS	3265	broad.mit.edu	37	11	533874	533874	+	Missense_Mutation	SNP	T	T	C	rs121913233		TCGA-EL-A3CZ-01A-11D-A19J-08	TCGA-EL-A3CZ-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	25c1a1a4-82e1-485a-afce-cafaed57945f	15fb2f33-0687-4679-b3b1-2244f979c0a7	g.chr11:533874T>C	ENST00000451590.1	-	3	369	c.182A>G	c.(181-183)cAg>cGg	p.Q61R	HRAS_ENST00000311189.7_Missense_Mutation_p.Q61R|HRAS_ENST00000468682.2_5'UTR|HRAS_ENST00000397596.2_Missense_Mutation_p.Q61R|HRAS_ENST00000417302.1_Missense_Mutation_p.Q61R|HRAS_ENST00000397594.1_Missense_Mutation_p.Q61R	NM_001130442.1|NM_005343.2	NP_001123914.1|NP_005334.1	P01112	RASH_HUMAN	Harvey rat sarcoma viral oncogene homolog	61			Q -> K (in follicular thyroid carcinoma samples; somatic mutation; increases transformation of cultured cell lines; dbSNP:rs28933406). {ECO:0000269|PubMed:12727991}.|Q -> L (in melanoma; strongly reduced GTP hydrolysis in the presence of RAF1; increases transformation of cultured cell lines).		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular senescence (GO:0090398)|chemotaxis (GO:0006935)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|intrinsic apoptotic signaling pathway (GO:0097193)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of cell differentiation (GO:0045596)|negative regulation of cell proliferation (GO:0008285)|negative regulation of gene expression (GO:0010629)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Rho GTPase activity (GO:0034259)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of JNK cascade (GO:0046330)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rac protein signal transduction (GO:0035022)|positive regulation of ruffle assembly (GO:1900029)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of wound healing (GO:0090303)|protein heterooligomerization (GO:0051291)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|protein C-terminus binding (GO:0008022)	p.Q61R(136)|p.Q61L(117)|p.Q61P(3)		adrenal_gland(1)|bone(3)|breast(7)|cervix(23)|endometrium(4)|haematopoietic_and_lymphoid_tissue(12)|kidney(1)|large_intestine(2)|liver(1)|lung(16)|oesophagus(2)|penis(2)|pituitary(10)|prostate(31)|salivary_gland(24)|skin(184)|soft_tissue(38)|stomach(14)|testis(5)|thymus(1)|thyroid(173)|upper_aerodigestive_tract(122)|urinary_tract(225)	901		all_cancers(49;4.37e-09)|all_epithelial(84;2.09e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;7.63e-28)|Epithelial(43;7.29e-27)|OV - Ovarian serous cystadenocarcinoma(40;7.15e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GTACTCCTCCTGGCCGGCGGT	0.597	Q61L(KNS62_LUNG)|Q61L(KYSE30_OESOPHAGUS)|Q61L(NCIH1915_LUNG)	6	Mis		"""infrequent sarcomas, rare other types"""	"""rhadomyosarcoma, ganglioneuroblastoma, bladder"""			Costello syndrome	HNSCC(11;0.0054)																												ENST00000417302.1	Q61L(KNS62_LUNG)|Q61L(KYSE30_OESOPHAGUS)|Q61L(NCIH1915_LUNG)	6	yes	Dom	yes	Costello syndrome	11	11p15.5	3265	Mis	v-Ha-ras Harvey rat sarcoma viral oncogene homolog			"""E, L, M"""		"""rhadomyosarcoma, ganglioneuroblastoma, bladder"""	"""infrequent sarcomas, rare other types"""		256	Substitution - Missense(256)	p.Q61R(136)|p.Q61L(117)|p.Q61P(3)	skin(70)|thyroid(58)|urinary_tract(53)|prostate(23)|upper_aerodigestive_tract(22)|lung(11)|salivary_gland(6)|haematopoietic_and_lymphoid_tissue(5)|testis(3)|liver(2)|cervix(1)|penis(1)|oesophagus(1)	adrenal_gland(1)|bone(3)|breast(7)|cervix(23)|endometrium(4)|haematopoietic_and_lymphoid_tissue(12)|kidney(1)|large_intestine(2)|liver(1)|lung(16)|oesophagus(2)|penis(2)|pituitary(10)|prostate(31)|salivary_gland(24)|skin(184)|soft_tissue(38)|stomach(14)|testis(5)|thymus(1)|thyroid(173)|upper_aerodigestive_tract(122)|urinary_tract(225)	901						c.(181-183)cAg>cGg		Harvey rat sarcoma viral oncogene homolog	Sulindac(DB00605)						117.0	102.0	107.0					11																	533874		2203	4300	6503	SO:0001583	missense	3265	Costello syndrome	Familial Cancer Database	incl.: Facio-Cutaneous-Skeletal syndrome	activation of MAPKK activity|axon guidance|blood coagulation|cell cycle arrest|cellular senescence|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|mitotic cell cycle G1/S transition checkpoint|negative regulation of cell proliferation|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of DNA replication|positive regulation of epithelial cell proliferation|Ras protein signal transduction|synaptic transmission	cytosol|Golgi membrane|plasma membrane	GTP binding|GTPase activity|protein C-terminus binding	g.chr11:533874T>C	AJ437024	CCDS7698.1, CCDS7699.1	11p15.5	2014-09-17	2013-07-08		ENSG00000174775	ENSG00000174775			5173	protein-coding gene	gene with protein product		190020	"""v-Ha-ras Harvey rat sarcoma viral oncogene homolog"""	HRAS1			Standard	NM_176795		Approved		uc010qvx.2	P01112	OTTHUMG00000131919	ENST00000451590.1:c.182A>G	11.37:g.533874T>C	ENSP00000407586:p.Gln61Arg	HNSCC(11;0.0054)				HRAS_ENST00000397594.1_Missense_Mutation_p.Q61R|HRAS_ENST00000468682.2_5'UTR|HRAS_ENST00000397596.2_Missense_Mutation_p.Q61R|HRAS_ENST00000451590.1_Missense_Mutation_p.Q61R|HRAS_ENST00000311189.7_Missense_Mutation_p.Q61R	p.Q61R	NM_176795.3	NP_789765.1	P01112	RASH_HUMAN		all cancers(45;7.63e-28)|Epithelial(43;7.29e-27)|OV - Ovarian serous cystadenocarcinoma(40;7.15e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)	3	369	-		all_cancers(49;4.37e-09)|all_epithelial(84;2.09e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)	61		Q -> K (in follicular thyroid carcinoma samples; somatic mutation; increases transformation of cultured cell lines; dbSNP:rs28933406).|Q -> L (in melanoma; strongly reduced GTP hydrolysis in the presence of RAF1; increases transformation of cultured cell lines).			B5BUA0|Q14080|Q6FHV9|Q9BR65|Q9UCE2	Missense_Mutation	SNP	ENST00000451590.1	37	c.182A>G	CCDS7698.1	.	.	.	.	.	.	.	.	.	.	T	14.48	2.546606	0.45383	.	.	ENSG00000174775	ENST00000397594;ENST00000397596;ENST00000451590;ENST00000417302;ENST00000311189	D;D;D;D;D	0.83673	-1.75;-1.75;-1.75;-1.75;-1.75	3.64	3.64	0.41730	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.85613	0.5737	M	0.90870	3.155	0.80722	D	1	B;B	0.21071	0.051;0.008	B;B	0.22152	0.022;0.038	D	0.85970	0.1476	10	0.66056	D	0.02	.	11.8872	0.52608	0.0:0.0:0.0:1.0	.	61;61	P01112-2;P01112	.;RASH_HUMAN	R	61	ENSP00000380722:Q61R;ENSP00000380723:Q61R;ENSP00000407586:Q61R;ENSP00000388246:Q61R;ENSP00000309845:Q61R	ENSP00000309845:Q61R	Q	-	2	0	HRAS	523874	1.000000	0.71417	0.985000	0.45067	0.482000	0.33219	7.727000	0.84838	1.662000	0.50781	0.459000	0.35465	CAG		0.597	HRAS-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259403.2	NM_176795		32	46	0	0	0	0.013726	0	32	46				
GNPAT	8443	broad.mit.edu	37	1	231411916	231411916	+	Missense_Mutation	SNP	C	C	T			TCGA-EL-A3CZ-01A-11D-A19J-08	TCGA-EL-A3CZ-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	25c1a1a4-82e1-485a-afce-cafaed57945f	15fb2f33-0687-4679-b3b1-2244f979c0a7	g.chr1:231411916C>T	ENST00000366647.4	+	15	2142	c.1973C>T	c.(1972-1974)gCc>gTc	p.A658V	GNPAT_ENST00000366646.3_Missense_Mutation_p.A597V|GNPAT_ENST00000469332.1_3'UTR	NM_014236.3	NP_055051.1	O15228	GNPAT_HUMAN	glyceronephosphate O-acyltransferase	658					cellular lipid metabolic process (GO:0044255)|cerebellum morphogenesis (GO:0021587)|ether lipid biosynthetic process (GO:0008611)|glycerophospholipid biosynthetic process (GO:0046474)|membrane organization (GO:0061024)|paranodal junction assembly (GO:0030913)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|response to drug (GO:0042493)|response to fatty acid (GO:0070542)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)|synapse assembly (GO:0007416)	membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	glycerone-phosphate O-acyltransferase activity (GO:0016287)|palmitoyl-CoA hydrolase activity (GO:0016290)|receptor binding (GO:0005102)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	23	Breast(184;0.0871)	all_cancers(173;0.2)|Prostate(94;0.183)				AATGAACCTGCCACAACCAAA	0.274																																						ENST00000366647.4																			0				breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	23						c.(1972-1974)gCc>gTc		glyceronephosphate O-acyltransferase							23.0	26.0	25.0					1																	231411916		2193	4292	6485	SO:0001583	missense	8443				ether lipid biosynthetic process|fatty acid metabolic process|organ morphogenesis	peroxisomal matrix|peroxisomal membrane	glycerone-phosphate O-acyltransferase activity	g.chr1:231411916C>T	AF043937	CCDS1592.1	1q42	2008-02-05			ENSG00000116906	ENSG00000116906	2.3.1.42		4416	protein-coding gene	gene with protein product		602744				9459311, 9536089	Standard	NM_014236		Approved	DHAPAT, DAPAT, DAP-AT	uc001hup.4	O15228	OTTHUMG00000038024	ENST00000366647.4:c.1973C>T	1.37:g.231411916C>T	ENSP00000355607:p.Ala658Val					GNPAT_ENST00000366646.3_Missense_Mutation_p.A597V|GNPAT_ENST00000469332.1_3'UTR	p.A658V	NM_014236.3	NP_055051.1	O15228	GNPAT_HUMAN			15	2142	+	Breast(184;0.0871)	all_cancers(173;0.2)|Prostate(94;0.183)	658					B4DNM9|Q5TBH7|Q9BWC2	Missense_Mutation	SNP	ENST00000366647.4	37	c.1973C>T	CCDS1592.1	.	.	.	.	.	.	.	.	.	.	C	18.07	3.542036	0.65198	.	.	ENSG00000116906	ENST00000366647;ENST00000366646	T;T	0.67698	-0.28;-0.23	4.98	4.98	0.66077	.	0.448742	0.24564	N	0.037441	T	0.63896	0.2550	L	0.59436	1.845	0.44254	D	0.9971	P;B	0.46621	0.881;0.245	B;B	0.40940	0.344;0.052	T	0.65442	-0.6167	10	0.34782	T	0.22	.	16.2152	0.82206	0.0:1.0:0.0:0.0	.	597;658	B4DNM9;O15228	.;GNPAT_HUMAN	V	658;597	ENSP00000355607:A658V;ENSP00000355606:A597V	ENSP00000355606:A597V	A	+	2	0	GNPAT	229478539	0.993000	0.37304	0.954000	0.39281	0.961000	0.63080	4.041000	0.57339	2.596000	0.87737	0.563000	0.77884	GCC		0.274	GNPAT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092871.1			4	17	0	0	0	0.009096	0	4	17				
PHIP	55023	broad.mit.edu	37	6	79707237	79707237	+	Missense_Mutation	SNP	G	G	A			TCGA-EL-A3CZ-01A-11D-A19J-08	TCGA-EL-A3CZ-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	25c1a1a4-82e1-485a-afce-cafaed57945f	15fb2f33-0687-4679-b3b1-2244f979c0a7	g.chr6:79707237G>A	ENST00000275034.4	-	19	2262	c.2095C>T	c.(2095-2097)Cgg>Tgg	p.R699W		NM_017934.5	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	699					cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(10)|kidney(4)|large_intestine(20)|lung(20)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	68		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)		TGCATTTGCCGTACACCTTCA	0.468																																						ENST00000275034.4																			0				NS(1)|breast(1)|central_nervous_system(2)|endometrium(10)|kidney(4)|large_intestine(20)|lung(20)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	68						c.(2095-2097)Cgg>Tgg		pleckstrin homology domain interacting protein							250.0	216.0	228.0					6																	79707237		2203	4300	6503	SO:0001583	missense	55023				insulin receptor signaling pathway|negative regulation of apoptosis|positive regulation of cell proliferation|positive regulation of insulin-like growth factor receptor signaling pathway|positive regulation of mitosis	nucleus	insulin receptor binding	g.chr6:79707237G>A	AF310250	CCDS4987.1	6q14	2013-01-09			ENSG00000146247	ENSG00000146247		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	15673	protein-coding gene	gene with protein product	"""DDB1 and CUL4 associated factor 14"""	612870		WDR11		11018022	Standard	NM_017934		Approved	ndrp, FLJ20705, DCAF14, BRWD2	uc003pir.3	Q8WWQ0	OTTHUMG00000015071	ENST00000275034.4:c.2095C>T	6.37:g.79707237G>A	ENSP00000275034:p.Arg699Trp						p.R699W	NM_017934.5	NP_060404.3	Q8WWQ0	PHIP_HUMAN		BRCA - Breast invasive adenocarcinoma(397;0.231)	19	2262	-		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)	699					A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Missense_Mutation	SNP	ENST00000275034.4	37	c.2095C>T	CCDS4987.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.055776	0.76074	.	.	ENSG00000146247	ENST00000275034	T	0.30981	1.51	4.96	3.99	0.46301	.	0.090653	0.44902	D	0.000417	T	0.42607	0.1210	M	0.62154	1.92	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.77557	0.99;0.99	T	0.27640	-1.0068	9	.	.	.	-9.4073	15.0895	0.72183	0.0:0.0:0.8485:0.1515	.	699;699	A7J992;Q8WWQ0	.;PHIP_HUMAN	W	699	ENSP00000275034:R699W	.	R	-	1	2	PHIP	79763956	1.000000	0.71417	0.987000	0.45799	0.995000	0.86356	6.204000	0.72143	2.264000	0.75181	0.655000	0.94253	CGG		0.468	PHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041297.2			31	55	0	0	0	0.010818	0	31	55				
BTRC	8945	broad.mit.edu	37	10	103292735	103292735	+	Silent	SNP	C	C	T			TCGA-EL-A3CZ-01A-11D-A19J-08	TCGA-EL-A3CZ-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	25c1a1a4-82e1-485a-afce-cafaed57945f	15fb2f33-0687-4679-b3b1-2244f979c0a7	g.chr10:103292735C>T	ENST00000370187.3	+	9	1123	c.1005C>T	c.(1003-1005)tgC>tgT	p.C335C	BTRC_ENST00000393441.4_Silent_p.C294C|BTRC_ENST00000408038.2_Silent_p.C299C	NM_033637.3	NP_378663.1	Q9Y297	FBW1A_HUMAN	beta-transducin repeat containing E3 ubiquitin protein ligase	335					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cellular response to organic cyclic compound (GO:0071407)|G2/M transition of mitotic cell cycle (GO:0000086)|mammary gland epithelial cell proliferation (GO:0033598)|mitotic cell cycle (GO:0000278)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of proteolysis (GO:0045862)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein dephosphorylation (GO:0006470)|protein destabilization (GO:0031648)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|regulation of cell cycle (GO:0051726)|regulation of circadian rhythm (GO:0042752)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|rhythmic process (GO:0048511)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|signal transduction (GO:0007165)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|SCF ubiquitin ligase complex (GO:0019005)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(4)|kidney(2)|large_intestine(6)|lung(11)|ovary(2)|stomach(1)|urinary_tract(1)	27		Colorectal(252;0.234)		Epithelial(162;1.05e-08)|all cancers(201;6.59e-07)		CATTGGAATGCAAGCGAATTC	0.438																																						ENST00000370187.3																			0				endometrium(4)|kidney(2)|large_intestine(6)|lung(11)|ovary(2)|stomach(1)|urinary_tract(1)	27						c.(1003-1005)tgC>tgT		beta-transducin repeat containing E3 ubiquitin protein ligase							175.0	148.0	157.0					10																	103292735		2203	4300	6503	SO:0001819	synonymous_variant	8945				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|positive regulation of proteolysis|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein destabilization|viral reproduction|Wnt receptor signaling pathway	cytosol|nucleus|SCF ubiquitin ligase complex		g.chr10:103292735C>T	Y14153	CCDS7511.1, CCDS7512.1, CCDS73183.1	10q24.32	2013-01-10	2012-02-23		ENSG00000166167	ENSG00000166167		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	1144	protein-coding gene	gene with protein product		603482	"""beta-transducin repeat containing"""			9660940, 10331953, 18354483	Standard	NM_033637		Approved	bTrCP, betaTrCP, FBXW1A, Fwd1, beta-TrCP1, bTrCP1	uc001kta.4	Q9Y297	OTTHUMG00000018932	ENST00000370187.3:c.1005C>T	10.37:g.103292735C>T						BTRC_ENST00000408038.2_Silent_p.C299C|BTRC_ENST00000393441.4_Silent_p.C294C	p.C335C	NM_033637.3	NP_378663.1	Q9Y297	FBW1A_HUMAN		Epithelial(162;1.05e-08)|all cancers(201;6.59e-07)	9	1123	+		Colorectal(252;0.234)	335					B5MD49|Q5W141|Q5W142|Q9Y213	Silent	SNP	ENST00000370187.3	37	c.1005C>T	CCDS7512.1																																																																																				0.438	BTRC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049936.1	NM_033637		6	90	0	0	0	0.001168	0	6	90				
RAPH1	65059	broad.mit.edu	37	2	204304820	204304821	+	Frame_Shift_Ins	INS	-	-	T			TCGA-EL-A3CZ-01A-11D-A19J-08	TCGA-EL-A3CZ-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	25c1a1a4-82e1-485a-afce-cafaed57945f	15fb2f33-0687-4679-b3b1-2244f979c0a7	g.chr2:204304820_204304821insT	ENST00000319170.5	-	14	3391_3392	c.3092_3093insA	c.(3091-3093)aatfs	p.N1031fs	RAPH1_ENST00000374493.3_Frame_Shift_Ins_p.N1083fs|RAPH1_ENST00000457812.1_Intron|ABI2_ENST00000295851.5_3'UTR	NM_213589.1	NP_998754.1	Q70E73	RAPH1_HUMAN	Ras association (RalGDS/AF-6) and pleckstrin homology domains 1	1031					axon extension (GO:0048675)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)				breast(5)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(7)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						CTCCAGAAAGATTGAGTTTTCC	0.545																																						ENST00000319170.5																			0				breast(5)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(7)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						c.(3091-3093)actfs		Ras association (RalGDS/AF-6) and pleckstrin homology domains 1																																				SO:0001589	frameshift_variant	65059				cell-matrix adhesion|signal transduction	cytoplasm|cytoskeleton|filopodium|lamellipodium|nucleus|plasma membrane		g.chr2:204304820_204304821insT	AJ584699	CCDS2359.1, CCDS2360.1	2q33	2013-01-10	2003-11-25	2003-11-26	ENSG00000173166	ENSG00000173166		"""Pleckstrin homology (PH) domain containing"""	14436	protein-coding gene	gene with protein product	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 18"""	609035	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 9"""	ALS2CR9, ALS2CR18			Standard	NM_203365		Approved	KIAA1681	uc002vad.3	Q70E73	OTTHUMG00000132876	ENST00000319170.5:c.3093dupA	2.37:g.204304822_204304822dupT	ENSP00000316543:p.Asn1031fs					RAPH1_ENST00000374493.3_Frame_Shift_Ins_p.T1083fs|RAPH1_ENST00000457812.1_Intron	p.T1031fs	NM_213589.1	NP_998754.1	Q70E73	RAPH1_HUMAN			14	3391_3392	-			1031					Q96Q37|Q9C0I2	Frame_Shift_Ins	INS	ENST00000319170.5	37	c.3092_3093insA	CCDS2359.1																																																																																				0.545	RAPH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256363.2	NM_025252		39	66						39	66	---	---	---	---
HMGB3P22	729595	broad.mit.edu	37	5	179121146	179121152	+	RNA	DEL	AAAAAAA	AAAAAAA	-	rs544126756|rs55708497	byFrequency	TCGA-EL-A3CZ-01A-11D-A19J-08	TCGA-EL-A3CZ-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	25c1a1a4-82e1-485a-afce-cafaed57945f	15fb2f33-0687-4679-b3b1-2244f979c0a7	g.chr5:179121146_179121152delAAAAAAA	ENST00000442010.2	+	0	253									high mobility group box 3 pseudogene 22																		actccgtctcaaaaaaaaaaaaaaaaa	0.483																																						ENST00000442010.2																			0																																																			0							g.chr5:179121146_179121152delAAAAAAA			5q35.3	2011-09-21	2011-04-05		ENSG00000225051	ENSG00000225051		"""High mobility group / HMG-box pseudogenes"""	39314	pseudogene	pseudogene			"""high-mobility group box 3 pseudogene 22"""			12727900	Standard	NG_028953		Approved				OTTHUMG00000163166		5.37:g.179121153_179121159delAAAAAAA														0	253	+									RNA	DEL	ENST00000442010.2	37																																																																																						0.483	HMGB3P22-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000371885.1			2	4						2	4	---	---	---	---
RP11-252A24.2	0	broad.mit.edu	37	16	74372915	74372915	+	RNA	DEL	T	T	-	rs397827801|rs11353924|rs532713769|rs398078750		TCGA-EL-A3CZ-01A-11D-A19J-08	TCGA-EL-A3CZ-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	25c1a1a4-82e1-485a-afce-cafaed57945f	15fb2f33-0687-4679-b3b1-2244f979c0a7	g.chr16:74372915delT	ENST00000429810.2	-	0	1404																											ACGTAGtttgttttttttttt	0.438																																						ENST00000429810.2																			0																																																			0							g.chr16:74372915delT																													16.37:g.74372915delT														0	1404	-									RNA	DEL	ENST00000429810.2	37																																																																																						0.438	RP11-252A24.2-003	KNOWN	basic	retained_intron	pseudogene	OTTHUMT00000434683.1			3	5						3	5	---	---	---	---
BAGE2	85319	broad.mit.edu	37	21	11085863	11085864	+	RNA	INS	-	-	C			TCGA-EL-A3CZ-01A-11D-A19J-08	TCGA-EL-A3CZ-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	25c1a1a4-82e1-485a-afce-cafaed57945f	15fb2f33-0687-4679-b3b1-2244f979c0a7	g.chr21:11085863_11085864insC	ENST00000470054.1	-	0	324							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2							extracellular region (GO:0005576)								Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		catcaccaccaccaccatcacc	0.579																																						ENST00000470054.1																			0													B melanoma antigen family, member 2																																						85319							g.chr21:11085863_11085864insC	AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172			15723	protein-coding gene	gene with protein product	"""cancer/testis antigen family 2, member 2"""					12461691	Standard	NM_182482		Approved	CT2.2		Q86Y30	OTTHUMG00000074128		21.37:g.11085865_11085865dupC												Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)	0	324	-								A8K925|Q08ER0	RNA	INS	ENST00000470054.1	37																																																																																						0.579	BAGE2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000157417.3	NM_182482		2	4						2	4	---	---	---	---
