#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
SIGLEC16	400709	broad.mit.edu	37	19	50474626	50474626	+	RNA	SNP	G	G	T			TCGA-EM-A4FH-01A-11D-A257-08	TCGA-EM-A4FH-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ad41f60-e79a-4db3-9c26-8e74cf80c34c	c93a2e43-26fb-461a-a9ab-60b52d591e61	g.chr19:50474626G>T	ENST00000602139.1	+	0	983							A6NMB1	SIG16_HUMAN	sialic acid binding Ig-like lectin 16 (gene/pseudogene)						cell adhesion (GO:0007155)|innate immune response (GO:0045087)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			endometrium(2)|kidney(2)|lung(6)	10						GCGAGCCCTGGACCTCTCTGT	0.667																																						ENST00000602139.1																			0				endometrium(2)|kidney(2)|lung(6)	10								sialic acid binding Ig-like lectin 16 (gene/pseudogene)																																						400709							g.chr19:50474626G>T	BC030222		19q13.33	2014-03-20	2008-08-04	2008-08-04	ENSG00000161643	ENSG00000161643		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"""	24851	protein-coding gene	gene with protein product			"""sialic acid binding Ig-like lectin, pseudogene 16"""	SIGLECP16		11986327, 18629938	Standard	NR_002825		Approved	Siglec-P16	uc002prf.3	A6NMB1	OTTHUMG00000183074		19.37:g.50474626G>T														0	983	+									RNA	SNP	ENST00000602139.1	37			.	.	.	.	.	.	.	.	.	.	G	13.19	2.162976	0.38217	.	.	ENSG00000161643	ENST00000417280;ENST00000456956	.	.	.	1.54	0.332	0.15938	.	1.079610	0.07174	N	0.852842	T	0.38188	0.1031	.	.	.	0.21841	N	0.999511	.	.	.	.	.	.	T	0.43180	-0.9407	6	0.72032	D	0.01	.	4.7778	0.13187	0.0:0.0:0.6367:0.3633	.	.	.	.	Y	348;320	.	ENSP00000396157:D348Y	D	+	1	0	SIGLEC16	55166438	0.001000	0.12720	0.357000	0.25798	0.528000	0.34623	-0.126000	0.10563	0.158000	0.19367	0.195000	0.17529	GAC		0.667	SIGLEC16-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000464979.1	NR_002825		29	60	1	0	6.53348e-20	1	7.72138e-20	29	60				
EFCAB14	9813	broad.mit.edu	37	1	47144234	47144234	+	Missense_Mutation	SNP	G	G	T			TCGA-EM-A4FH-01A-11D-A257-08	TCGA-EM-A4FH-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ad41f60-e79a-4db3-9c26-8e74cf80c34c	c93a2e43-26fb-461a-a9ab-60b52d591e61	g.chr1:47144234G>T	ENST00000371933.3	-	11	2363	c.1387C>A	c.(1387-1389)Cta>Ata	p.L463I	EFCAB14_ENST00000544071.1_Intron|EFCAB14-AS1_ENST00000442839.1_RNA|EFCAB14-AS1_ENST00000418985.1_RNA	NM_014774.2	NP_055589.1	O75071	EFC14_HUMAN	EF-hand calcium binding domain 14	463	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.						calcium ion binding (GO:0005509)										GCAGAACCTAGGGAGGTCCAG	0.453																																						ENST00000371933.3																			0											c.(1387-1389)Cta>Ata		EF-hand calcium binding domain 14							100.0	99.0	99.0					1																	47144234		2203	4300	6503	SO:0001583	missense	9813							g.chr1:47144234G>T	AB007963	CCDS30706.1	1p33	2013-01-10	2012-11-29	2012-11-29	ENSG00000159658	ENSG00000159658		"""EF-hand domain containing"""	29051	protein-coding gene	gene with protein product			"""KIAA0494"""	KIAA0494		9455484	Standard	NM_014774		Approved		uc001cqk.4	O75071	OTTHUMG00000007992	ENST00000371933.3:c.1387C>A	1.37:g.47144234G>T	ENSP00000361001:p.Leu463Ile					EFCAB14_ENST00000544071.1_Intron|EFCAB14-AS1_ENST00000442839.1_RNA|EFCAB14-AS1_ENST00000418985.1_RNA	p.L463I	NM_014774.2	NP_055589.1					11	2363	-								D3DQ23|Q5SXB8	Missense_Mutation	SNP	ENST00000371933.3	37	c.1387C>A	CCDS30706.1	.	.	.	.	.	.	.	.	.	.	G	17.03	3.283485	0.59867	.	.	ENSG00000159658	ENST00000371933	T	0.09630	2.96	5.14	0.91	0.19337	EF-hand-like domain (1);	0.106420	0.46758	D	0.000275	T	0.22044	0.0531	L	0.59436	1.845	0.32425	N	0.548889	D;P	0.71674	0.998;0.932	D;P	0.83275	0.996;0.546	T	0.12915	-1.0529	10	0.56958	D	0.05	-0.7985	5.5152	0.16902	0.5191:0.1482:0.3327:0.0	.	255;463	B7Z3D1;O75071	.;K0494_HUMAN	I	463	ENSP00000361001:L463I	ENSP00000361001:L463I	L	-	1	2	KIAA0494	46916821	0.996000	0.38824	0.659000	0.29680	0.975000	0.68041	0.406000	0.21032	-0.002000	0.14469	0.591000	0.81541	CTA		0.453	EFCAB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021931.1	NM_014774		17	42	1	0	3.51602e-12	1	3.97463e-12	17	42				
CNST	163882	broad.mit.edu	37	1	246810626	246810626	+	Missense_Mutation	SNP	A	A	T			TCGA-EM-A4FH-01A-11D-A257-08	TCGA-EM-A4FH-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ad41f60-e79a-4db3-9c26-8e74cf80c34c	c93a2e43-26fb-461a-a9ab-60b52d591e61	g.chr1:246810626A>T	ENST00000366513.4	+	9	1392	c.1123A>T	c.(1123-1125)Acc>Tcc	p.T375S	CNST_ENST00000366512.3_Missense_Mutation_p.T375S|CNST_ENST00000483271.1_3'UTR	NM_152609.2	NP_689822.2	Q6PJW8	CNST_HUMAN	consortin, connexin sorting protein	375					negative regulation of phosphatase activity (GO:0010923)|positive regulation of Golgi to plasma membrane protein transport (GO:0042998)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|trans-Golgi network (GO:0005802)|transport vesicle (GO:0030133)	connexin binding (GO:0071253)|phosphatase binding (GO:0019902)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|prostate(1)|urinary_tract(2)	28						AGCGCTCCACACCCAGTCCTC	0.587											OREG0014367	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										ENST00000366513.4																			0				breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|prostate(1)|urinary_tract(2)	28						c.(1123-1125)Acc>Tcc		consortin, connexin sorting protein							87.0	91.0	89.0					1																	246810626		2203	4300	6503	SO:0001583	missense	163882				positive regulation of Golgi to plasma membrane protein transport	integral to membrane|plasma membrane|protein complex|trans-Golgi network|transport vesicle	connexin binding	g.chr1:246810626A>T	AK056563	CCDS1628.1, CCDS44343.1	1q44	2012-04-17	2009-11-03	2009-11-03	ENSG00000162852	ENSG00000162852		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	26486	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 64"""	613439	"""chromosome 1 open reading frame 71"""	C1orf71		19864490	Standard	NM_152609		Approved	FLJ32001, PPP1R64	uc001ibp.3	Q6PJW8	OTTHUMG00000040090	ENST00000366513.4:c.1123A>T	1.37:g.246810626A>T	ENSP00000355470:p.Thr375Ser		OREG0014367	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	2468	CNST_ENST00000483271.1_3'UTR|CNST_ENST00000366512.3_Missense_Mutation_p.T375S	p.T375S	NM_152609.2	NP_689822.2	Q6PJW8	CNST_HUMAN			9	1392	+			375					Q5VSY9|Q5VTM7|Q8IYA9|Q8N3L5|Q8NB09|Q8TEI2|Q96MR5	Missense_Mutation	SNP	ENST00000366513.4	37	c.1123A>T	CCDS1628.1	.	.	.	.	.	.	.	.	.	.	A	15.26	2.780145	0.49891	.	.	ENSG00000162852	ENST00000366513;ENST00000366512	T;T	0.26660	1.87;1.72	5.5	-1.96	0.07525	.	0.316496	0.29876	N	0.010965	T	0.27384	0.0672	M	0.66939	2.045	0.80722	D	1	P;P	0.47841	0.767;0.901	B;P	0.45276	0.359;0.475	T	0.19418	-1.0306	10	0.48119	T	0.1	-8.6879	10.9091	0.47097	0.7769:0.0:0.2231:0.0	.	375;375	Q6PJW8;Q6PJW8-2	CNST_HUMAN;.	S	375	ENSP00000355470:T375S;ENSP00000355469:T375S	ENSP00000355469:T375S	T	+	1	0	CNST	244877249	1.000000	0.71417	0.995000	0.50966	0.268000	0.26511	0.532000	0.23067	-0.133000	0.11537	0.383000	0.25322	ACC		0.587	CNST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096780.1	NM_152609		50	55	0	0	0	1	0	50	55				
TBP	6908	broad.mit.edu	37	6	170871088	170871088	+	Silent	SNP	G	G	A			TCGA-EM-A4FH-01A-11D-A257-08	TCGA-EM-A4FH-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ad41f60-e79a-4db3-9c26-8e74cf80c34c	c93a2e43-26fb-461a-a9ab-60b52d591e61	g.chr6:170871088G>A	ENST00000392092.2	+	3	543	c.264G>A	c.(262-264)caG>caA	p.Q88Q	TBP_ENST00000540980.1_Silent_p.Q68Q|TBP_ENST00000230354.6_Silent_p.Q88Q	NM_003194.4	NP_003185.1	P20226	TBP_HUMAN	TATA box binding protein	88	Poly-Gln.				cell death (GO:0008219)|gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|transcription factor TFIIA complex (GO:0005672)|transcription factor TFIID complex (GO:0005669)	repressing transcription factor binding (GO:0070491)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.Q88Q(1)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(1)	26		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591)		agcagcagcagcagcagcagc	0.612																																						ENST00000392092.2																			1	Substitution - coding silent(1)	p.Q88Q(1)	urinary_tract(1)	breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(1)	26						c.(262-264)caG>caA		TATA box binding protein																																				SO:0001819	synonymous_variant	6908				cell death|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|viral reproduction	transcription factor TFIIA complex|transcription factor TFIID complex	repressing transcription factor binding|transcription regulatory region DNA binding	g.chr6:170871088G>A	M55654	CCDS5315.1, CCDS55077.1	6q27	2014-04-02			ENSG00000112592	ENSG00000112592		"""General transcription factors"""	11588	protein-coding gene	gene with protein product		600075		GTF2D1, SCA17		2194289, 11448935	Standard	NM_003194		Approved	TFIID	uc003qxu.3	P20226	OTTHUMG00000016084	ENST00000392092.2:c.264G>A	6.37:g.170871088G>A						TBP_ENST00000540980.1_Silent_p.Q68Q|TBP_ENST00000230354.6_Silent_p.Q88Q	p.Q88Q	NM_003194.4	NP_003185.1	P20226	TBP_HUMAN		OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591)	3	543	+		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)	88			Poly-Gln.		B4E3B3|F5H869|Q16845|Q6IBM6|Q9UC02	Silent	SNP	ENST00000392092.2	37	c.264G>A	CCDS5315.1																																																																																				0.612	TBP-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043271.2	NM_003194		5	55	0	0	0	1	0	5	55				
TRIOBP	11078	broad.mit.edu	37	22	38119859	38119859	+	Silent	SNP	C	C	T	rs66505048	byFrequency	TCGA-EM-A4FH-01A-11D-A257-08	TCGA-EM-A4FH-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ad41f60-e79a-4db3-9c26-8e74cf80c34c	c93a2e43-26fb-461a-a9ab-60b52d591e61	g.chr22:38119859C>T	ENST00000406386.3	+	7	1551	c.1296C>T	c.(1294-1296)tgC>tgT	p.C432C		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	432					actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)	p.C432C(6)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					GAACATCCTGCGCCCAGCGGG	0.582																																						ENST00000406386.3																			6	Substitution - coding silent(6)	p.C432C(6)	kidney(3)|cervix(1)|lung(1)|endometrium(1)	central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12						c.(1294-1296)tgC>tgT		TRIO and F-actin binding protein																																				SO:0001819	synonymous_variant	11078				actin modification|barbed-end actin filament capping	actin cytoskeleton|cytoplasm|nucleus	actin binding|GTP-Rho binding|myosin II binding|protein binding|ubiquitin protein ligase binding	g.chr22:38119859C>T	AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"""Pleckstrin homology (PH) domain containing"""	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.1296C>T	22.37:g.38119859C>T						RP1-37E16.12_ENST00000455236.1_RNA	p.C432C	NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN			7	1551	+	Melanoma(58;0.0574)		432					B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Silent	SNP	ENST00000406386.3	37	c.1296C>T	CCDS43015.1																																																																																				0.582	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2			4	104	0	0	0	1	0	4	104				
ARRB2	409	broad.mit.edu	37	17	4619828	4619828	+	Silent	SNP	A	A	C			TCGA-EM-A4FH-01A-11D-A257-08	TCGA-EM-A4FH-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ad41f60-e79a-4db3-9c26-8e74cf80c34c	c93a2e43-26fb-461a-a9ab-60b52d591e61	g.chr17:4619828A>C	ENST00000269260.2	+	5	515	c.282A>C	c.(280-282)ccA>ccC	p.P94P	ARRB2_ENST00000571206.1_5'UTR|ARRB2_ENST00000381488.6_Silent_p.P79P|ARRB2_ENST00000570718.1_3'UTR|ARRB2_ENST00000575877.1_Silent_p.P94P|ARRB2_ENST00000346341.2_Silent_p.P79P|ARRB2_ENST00000412477.3_Silent_p.P94P|ARRB2_ENST00000572457.1_5'UTR|ARRB2_ENST00000574954.1_5'UTR	NM_001257328.1|NM_001257330.1|NM_004313.3	NP_001244257.1|NP_001244259.1|NP_004304.1	P32121	ARRB2_HUMAN	arrestin, beta 2	94					adult walking behavior (GO:0007628)|apoptotic DNA fragmentation (GO:0006309)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cell chemotaxis (GO:0060326)|desensitization of G-protein coupled receptor protein signaling pathway by arrestin (GO:0002032)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|follicle-stimulating hormone signaling pathway (GO:0042699)|G-protein coupled receptor internalization (GO:0002031)|negative regulation of GTPase activity (GO:0034260)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of natural killer cell mediated cytotoxicity (GO:0045953)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|negative regulation of tumor necrosis factor production (GO:0032720)|Notch signaling pathway (GO:0007219)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of receptor internalization (GO:0002092)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of synaptic transmission, dopaminergic (GO:0032226)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|receptor internalization (GO:0031623)|regulation of androgen receptor signaling pathway (GO:0060765)|transcription from RNA polymerase II promoter (GO:0006366)|transforming growth factor beta receptor signaling pathway (GO:0007179)	basolateral plasma membrane (GO:0016323)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|endocytic vesicle (GO:0030139)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	angiotensin receptor binding (GO:0031701)|enzyme binding (GO:0019899)|G-protein coupled receptor binding (GO:0001664)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)|ubiquitin protein ligase binding (GO:0031625)			large_intestine(1)|liver(2)|lung(3)|prostate(1)	7						TGCCCAACCCACCCCGGCCCC	0.667																																						ENST00000269260.2																			0				large_intestine(1)|liver(2)|lung(3)|prostate(1)	7						c.(280-282)ccA>ccC		arrestin, beta 2							30.0	25.0	26.0					17																	4619828		2203	4298	6501	SO:0001819	synonymous_variant	409				cell chemotaxis|desensitization of G-protein coupled receptor protein signaling pathway by arrestin|G-protein coupled receptor internalization|negative regulation of natural killer cell mediated cytotoxicity|negative regulation of NF-kappaB transcription factor activity|negative regulation of protein ubiquitination|platelet activation|positive regulation of ERK1 and ERK2 cascade|proteasomal ubiquitin-dependent protein catabolic process|protein transport|protein ubiquitination|transcription from RNA polymerase II promoter|transforming growth factor beta receptor signaling pathway	coated pit|cytoplasmic membrane-bounded vesicle|cytosol|nucleus|plasma membrane	angiotensin receptor binding|ubiquitin protein ligase binding	g.chr17:4619828A>C		CCDS11050.1, CCDS11051.1, CCDS58504.1, CCDS58505.1, CCDS59276.1	17p13	2008-12-11			ENSG00000141480	ENSG00000141480			712	protein-coding gene	gene with protein product	"""arrestin 3"""	107941		ARR2		7695743	Standard	NM_001257329		Approved	BARR2, DKFZp686L0365	uc002fyl.3	P32121	OTTHUMG00000090759	ENST00000269260.2:c.282A>C	17.37:g.4619828A>C						ARRB2_ENST00000412477.3_Silent_p.P94P|ARRB2_ENST00000381488.6_Silent_p.P79P|ARRB2_ENST00000572457.1_5'UTR|ARRB2_ENST00000346341.2_Silent_p.P79P|ARRB2_ENST00000575877.1_Silent_p.P94P|ARRB2_ENST00000571206.1_5'UTR|ARRB2_ENST00000574954.1_5'UTR|ARRB2_ENST00000570718.1_3'UTR	p.P94P	NM_001257328.1|NM_001257330.1|NM_004313.3	NP_001244257.1|NP_001244259.1|NP_004304.1	P32121	ARRB2_HUMAN			5	515	+			94					B4DLW0|B5B0C0|B7WPL3|D3DTK2|H0Y688|Q0Z8D3|Q2PP19|Q6ICT3|Q8N7Y2|Q9UEQ6	Silent	SNP	ENST00000269260.2	37	c.282A>C	CCDS11050.1																																																																																				0.667	ARRB2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439552.1	NM_004313		5	16	0	0	0	1	0	5	16				
CXCL3	2921	broad.mit.edu	37	4	74904084	74904084	+	Silent	SNP	C	C	T			TCGA-EM-A4FH-01A-11D-A257-08	TCGA-EM-A4FH-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ad41f60-e79a-4db3-9c26-8e74cf80c34c	c93a2e43-26fb-461a-a9ab-60b52d591e61	g.chr4:74904084C>T	ENST00000296026.4	-	2	224	c.147G>A	c.(145-147)ctG>ctA	p.L49L	CXCL3_ENST00000511669.1_5'UTR	NM_002090.2	NP_002081.2	P19876	CXCL3_HUMAN	chemokine (C-X-C motif) ligand 3	49					immune response (GO:0006955)|inflammatory response (GO:0006954)|neutrophil chemotaxis (GO:0030593)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	chemokine activity (GO:0008009)			central_nervous_system(1)|endometrium(1)	2	Breast(15;0.00612)		all cancers(17;0.00273)|Lung(101;0.196)			GAATTCCCTGCAGTGTCTGCA	0.612																																						ENST00000296026.4																			0				central_nervous_system(1)|endometrium(1)	2						c.(145-147)ctG>ctA		chemokine (C-X-C motif) ligand 3							91.0	97.0	95.0					4																	74904084		2203	4300	6503	SO:0001819	synonymous_variant	2921				immune response|inflammatory response|neutrophil chemotaxis	extracellular space	chemokine activity	g.chr4:74904084C>T	M36821	CCDS34007.1	4q21	2013-02-25	2002-08-22	2002-08-23		ENSG00000163734		"""Endogenous ligands"""	4604	protein-coding gene	gene with protein product		139111	"""GRO3 oncogene"""	GRO3		2217207	Standard	NM_002090		Approved	SCYB3, GROg, MIP-2b, CINC-2b	uc003hhl.3	P19876		ENST00000296026.4:c.147G>A	4.37:g.74904084C>T						CXCL3_ENST00000511669.1_5'UTR	p.L49L	NM_002090.2	NP_002081.2	P19876	CXCL3_HUMAN	all cancers(17;0.00273)|Lung(101;0.196)		2	224	-	Breast(15;0.00612)		49					Q4W5H9	Silent	SNP	ENST00000296026.4	37	c.147G>A	CCDS34007.1																																																																																				0.612	CXCL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362721.1			10	119	0	0	0	1	0	10	119				
GLIS3	169792	broad.mit.edu	37	9	4118110	4118110	+	Silent	SNP	T	T	G			TCGA-EM-A4FH-01A-11D-A257-08	TCGA-EM-A4FH-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ad41f60-e79a-4db3-9c26-8e74cf80c34c	c93a2e43-26fb-461a-a9ab-60b52d591e61	g.chr9:4118110T>G	ENST00000324333.10	-	3	1096	c.903A>C	c.(901-903)ccA>ccC	p.P301P	GLIS3_ENST00000381971.3_Silent_p.P456P	NM_152629.3	NP_689842.3	Q8NEA6	GLIS3_HUMAN	GLIS family zinc finger 3	301	Pro-rich.		P -> Q (in dbSNP:rs6415788). {ECO:0000269|PubMed:15489334}.		negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(12)|lung(4)|ovary(2)|prostate(1)|skin(1)	26		Acute lymphoblastic leukemia(2;0.00464)|Breast(48;0.148)		Lung(2;0.00163)|GBM - Glioblastoma multiforme(50;0.00301)|LUSC - Lung squamous cell carcinoma(2;0.0148)		gtggggggcctgggggcggcg	0.731																																						ENST00000324333.10																			0				NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(12)|lung(4)|ovary(2)|prostate(1)|skin(1)	26						c.(901-903)ccA>ccC		GLIS family zinc finger 3							8.0	11.0	10.0					9																	4118110		1835	3769	5604	SO:0001819	synonymous_variant	169792				negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter		DNA binding|zinc ion binding	g.chr9:4118110T>G	BC033899	CCDS6451.1, CCDS43784.1	9p24.2	2008-05-02	2004-07-16	2004-07-16	ENSG00000107249	ENSG00000107249		"""Zinc fingers, C2H2-type"""	28510	protein-coding gene	gene with protein product		610192	"""zinc finger protein 515"""	ZNF515		14500813	Standard	NM_152629		Approved	MGC33662	uc003zhx.1	Q8NEA6	OTTHUMG00000019463	ENST00000324333.10:c.903A>C	9.37:g.4118110T>G						GLIS3_ENST00000381971.3_Silent_p.P456P	p.P301P	NM_152629.3	NP_689842.3	Q8NEA6	GLIS3_HUMAN		Lung(2;0.00163)|GBM - Glioblastoma multiforme(50;0.00301)|LUSC - Lung squamous cell carcinoma(2;0.0148)	3	1096	-		Acute lymphoblastic leukemia(2;0.00464)|Breast(48;0.148)	301		P -> Q (in dbSNP:rs6415788).	Pro-rich.		B1AL19|Q1PHK5	Silent	SNP	ENST00000324333.10	37	c.903A>C	CCDS6451.1																																																																																				0.731	GLIS3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051559.1	NM_152629		6	15	0	0	0	1	0	6	15				
RPS2	6187	broad.mit.edu	37	16	2013180	2013180	+	Missense_Mutation	SNP	C	C	A			TCGA-EM-A4FH-01A-11D-A257-08	TCGA-EM-A4FH-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ad41f60-e79a-4db3-9c26-8e74cf80c34c	c93a2e43-26fb-461a-a9ab-60b52d591e61	g.chr16:2013180C>A	ENST00000343262.4	-	4	401	c.345G>T	c.(343-345)caG>caT	p.Q115H	RPS2_ENST00000526522.1_Missense_Mutation_p.Q115H|SNORA10_ENST00000384084.1_RNA|SNHG9_ENST00000459373.1_lincRNA|SNORA64_ENST00000384674.1_RNA|RPS2_ENST00000530225.1_Missense_Mutation_p.Q115H|RPS2_ENST00000529806.1_Missense_Mutation_p.Q85H	NM_002952.3	NP_002943.2	P15880	RS2_HUMAN	ribosomal protein S2	115	S5 DRBM. {ECO:0000255|PROSITE- ProRule:PRU00268}.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of transferase activity (GO:0051347)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|fibroblast growth factor binding (GO:0017134)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|urinary_tract(2)	7						CGGCACGGGTCTGCTTCTGCA	0.542																																						ENST00000529806.1																			0				endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|urinary_tract(2)	7						c.(253-255)caG>caT		ribosomal protein S2							9.0	12.0	11.0					16																	2013180		2192	4289	6481	SO:0001583	missense	6187				endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic small ribosomal subunit|nucleoplasm	fibroblast growth factor 1 binding|fibroblast growth factor 3 binding|RNA binding|structural constituent of ribosome	g.chr16:2013180C>A	AB007147	CCDS10452.1	16p13.3	2011-04-05			ENSG00000140988	ENSG00000140988		"""S ribosomal proteins"""	10404	protein-coding gene	gene with protein product		603624				9582194	Standard	NM_002952		Approved	LLREP3, S2	uc002cno.2	P15880	OTTHUMG00000128708	ENST00000343262.4:c.345G>T	16.37:g.2013180C>A	ENSP00000341885:p.Gln115His					RPS2_ENST00000526522.1_Missense_Mutation_p.Q115H|RPS2_ENST00000343262.4_Missense_Mutation_p.Q115H|RPS2_ENST00000530225.1_Missense_Mutation_p.Q115H	p.Q85H			P15880	RS2_HUMAN			2	441	-			115					B2R5G0|D3DU82|Q3MIB1	Missense_Mutation	SNP	ENST00000343262.4	37	c.255G>T	CCDS10452.1	.	.	.	.	.	.	.	.	.	.	c	12.48	1.951739	0.34471	.	.	ENSG00000140988	ENST00000526522;ENST00000530225;ENST00000343262;ENST00000529806;ENST00000527302	.	.	.	3.91	1.87	0.25490	Ribosomal protein S5, N-terminal (2);Double-stranded RNA-binding-like (1);	0.000000	0.64402	U	0.000002	D	0.84138	0.5406	H	0.95574	3.69	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.79784	0.993;0.95	D	0.85289	0.1066	9	0.66056	D	0.02	.	9.2417	0.37500	0.0:0.8166:0.0:0.1834	.	115;115	P15880;E9PQD7	RS2_HUMAN;.	H	115;115;115;85;115	.	ENSP00000341885:Q115H	Q	-	3	2	RPS2	1953181	1.000000	0.71417	1.000000	0.80357	0.807000	0.45602	2.928000	0.48908	0.884000	0.36064	0.454000	0.30748	CAG		0.542	RPS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250613.2	NM_002952		6	6	1	0	3.59834e-05	1	3.8982e-05	6	6				
RBM10	8241	broad.mit.edu	37	X	47039364	47039364	+	Silent	SNP	C	C	A			TCGA-EM-A4FH-01A-11D-A257-08	TCGA-EM-A4FH-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ad41f60-e79a-4db3-9c26-8e74cf80c34c	c93a2e43-26fb-461a-a9ab-60b52d591e61	g.chrX:47039364C>A	ENST00000377604.3	+	10	1729	c.987C>A	c.(985-987)tcC>tcA	p.S329S	RBM10_ENST00000329236.7_Silent_p.S252S|RBM10_ENST00000345781.6_Silent_p.S252S|RBM10_ENST00000478410.1_3'UTR	NM_001204467.1|NM_001204468.1|NM_005676.4	NP_001191396.1|NP_001191397.1|NP_005667.2	P98175	RBM10_HUMAN	RNA binding motif protein 10	329	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				3'-UTR-mediated mRNA stabilization (GO:0070935)|mRNA processing (GO:0006397)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|large_intestine(10)|liver(1)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	48						TGTCCTCCTCCAACGTGCGCG	0.622																																					Melanoma(171;120 2705 19495 39241)	ENST00000377604.3																			0				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|large_intestine(10)|liver(1)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	48						c.(985-987)tcC>tcA		RNA binding motif protein 10							50.0	36.0	41.0					X																	47039364		2203	4300	6503	SO:0001819	synonymous_variant	8241				mRNA processing|RNA splicing	chromatin remodeling complex	nucleotide binding|RNA binding|zinc ion binding	g.chrX:47039364C>A	U35373	CCDS14274.1, CCDS56600.1, CCDS75969.1	Xp11.3	2014-06-09			ENSG00000182872	ENSG00000182872		"""Zinc fingers, RAN-binding domain containing"", ""G patch domain containing"", ""RNA binding motif (RRM) containing"""	9896	protein-coding gene	gene with protein product		300080				8590280, 8808293	Standard	NM_005676		Approved	DXS8237E, KIAA0122, GPATC9, ZRANB5, GPATCH9	uc004dhi.3	P98175	OTTHUMG00000021432	ENST00000377604.3:c.987C>A	X.37:g.47039364C>A						RBM10_ENST00000329236.7_Silent_p.S252S|RBM10_ENST00000345781.6_Silent_p.S252S|RBM10_ENST00000468791.1_Intron	p.S329S	NM_001204467.1|NM_001204468.1|NM_005676.4	NP_001191396.1|NP_001191397.1|NP_005667.2	P98175	RBM10_HUMAN			10	1729	+			329			RRM 2.		C4AM81|Q14136|Q5JRR2|Q9BTE4|Q9BTX0|Q9NTB1	Silent	SNP	ENST00000377604.3	37	c.987C>A	CCDS14274.1																																																																																				0.622	RBM10-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056381.1	NM_005676		3	21	1	0	0.004672	1	0.004672	3	21				
SPESP1	246777	broad.mit.edu	37	15	69222942	69222942	+	De_novo_Start_OutOfFrame	SNP	G	G	A			TCGA-EM-A4FH-01A-11D-A257-08	TCGA-EM-A4FH-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ad41f60-e79a-4db3-9c26-8e74cf80c34c	c93a2e43-26fb-461a-a9ab-60b52d591e61	g.chr15:69222942G>A	ENST00000310673.3	+	0	104				NOX5_ENST00000260364.5_De_novo_Start_InFrame|SPESP1_ENST00000560188.1_Intron|RP11-809H16.2_ENST00000557966.1_RNA|NOX5_ENST00000455873.3_5'Flank|NOX5_ENST00000448182.3_De_novo_Start_InFrame	NM_145658.3	NP_663633.1	Q6UW49	SPESP_HUMAN	sperm equatorial segment protein 1						acrosome reaction (GO:0007340)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organismal development (GO:0007275)	acrosomal vesicle (GO:0001669)				breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(11)|prostate(1)|skin(1)|urinary_tract(1)	19						TTCCCAGCCTGGTGGCCCCAG	0.622																																						ENST00000310673.3																			0				breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(11)|prostate(1)|skin(1)|urinary_tract(1)	19								sperm equatorial segment protein 1							234.0	179.0	198.0					15																	69222942		2200	4298	6498			246777				multicellular organismal development	acrosomal vesicle		g.chr15:69222942G>A	AF275321	CCDS10230.1	15q22.31	2011-04-15				ENSG00000258484			15570	protein-coding gene	gene with protein product		609399				12773409	Standard	NM_145658		Approved	SP-ESP	uc002arn.2	Q6UW49		ENST00000310673.3:c.-51G>A	15.37:g.69222942G>A						NOX5_ENST00000260364.5_De_novo_Start_InFrame|RP11-809H16.2_ENST00000557966.1_RNA|SPESP1_ENST00000560188.1_Intron|NOX5_ENST00000448182.3_De_novo_Start_InFrame		NM_145658.3	NP_663633.1	Q6UW49	SPESP_HUMAN			0	104	+								Q8NG22|Q8WVH8	Translation_Start_Site	SNP	ENST00000310673.3	37		CCDS10230.1																																																																																				0.622	SPESP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257125.1	NM_145658		8	75	0	0	0	1	0	8	75				
PAX8	7849	broad.mit.edu	37	2	114002079	114002079	+	Missense_Mutation	SNP	C	C	A			TCGA-EM-A4FH-01A-11D-A257-08	TCGA-EM-A4FH-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ad41f60-e79a-4db3-9c26-8e74cf80c34c	c93a2e43-26fb-461a-a9ab-60b52d591e61	g.chr2:114002079C>A	ENST00000429538.3	-	4	508	c.314G>T	c.(313-315)tGg>tTg	p.W105L	AC016683.6_ENST00000333145.5_RNA|AC016683.6_ENST00000445745.1_RNA|PAX8_ENST00000263334.5_Missense_Mutation_p.W105L|AC016683.6_ENST00000422956.2_RNA|PAX8_ENST00000263335.7_Missense_Mutation_p.W105L|AC016683.6_ENST00000451179.1_RNA|PAX8_ENST00000348715.5_Missense_Mutation_p.W105L|AC016683.6_ENST00000553869.2_RNA|PAX8_ENST00000397647.3_Missense_Mutation_p.W105L|AC016683.6_ENST00000556070.1_RNA|AC016683.6_ENST00000436293.2_RNA	NM_003466.3	NP_003457.1	Q06710	PAX8_HUMAN	paired box 8	105	Paired. {ECO:0000255|PROSITE- ProRule:PRU00381}.				anatomical structure morphogenesis (GO:0009653)|branching involved in ureteric bud morphogenesis (GO:0001658)|cellular response to gonadotropin stimulus (GO:0071371)|central nervous system development (GO:0007417)|inner ear morphogenesis (GO:0042472)|kidney development (GO:0001822)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|mesonephros development (GO:0001823)|metanephric comma-shaped body morphogenesis (GO:0072278)|metanephric distal convoluted tubule development (GO:0072221)|metanephric epithelium development (GO:0072207)|metanephric nephron tubule formation (GO:0072289)|metanephric S-shaped body morphogenesis (GO:0072284)|negative regulation of apoptotic process involved in metanephric collecting duct development (GO:1900215)|negative regulation of apoptotic process involved in metanephric nephron tubule development (GO:1900218)|negative regulation of mesenchymal cell apoptotic process involved in metanephric nephron morphogenesis (GO:0072305)|negative regulation of mesenchymal cell apoptotic process involved in metanephros development (GO:1900212)|otic vesicle development (GO:0071599)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0072108)|positive regulation of metanephric DCT cell differentiation (GO:2000594)|positive regulation of thyroid hormone generation (GO:2000611)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephric field specification (GO:0039003)|pronephros development (GO:0048793)|regulation of apoptotic process (GO:0042981)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)|regulation of thyroid-stimulating hormone secretion (GO:2000612)|thyroid gland development (GO:0030878)|thyroid-stimulating hormone signaling pathway (GO:0038194)|transcription, DNA-templated (GO:0006351)|urogenital system development (GO:0001655)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|thyroid-stimulating hormone receptor activity (GO:0004996)|transcription regulatory region DNA binding (GO:0044212)		PAX8/PPARG(117)	breast(1)|endometrium(4)|kidney(2)|large_intestine(1)|liver(1)|lung(9)|ovary(1)|skin(1)	20						TCGGATCTCCCAGGCAAACAT	0.582			T	PPARG	follicular thyroid		Thyroid dysgenesis																														Ovarian(188;7 2067 9084 29802 29892)	ENST00000429538.3				Dom	yes		2	2q12-q14	7849	T	paired box gene 8	yes	Thyroid dysgenesis	E	PPARG		follicular thyroid	PAX8/PPARG(117)	0				breast(1)|endometrium(4)|kidney(2)|large_intestine(1)|liver(1)|lung(9)|ovary(1)|skin(1)	20						c.(313-315)tGg>tTg		paired box 8							174.0	193.0	187.0					2																	114002079		2200	4299	6499	SO:0001583	missense	7849				branching involved in ureteric bud morphogenesis|cellular response to gonadotropin stimulus|central nervous system development|mesenchymal to epithelial transition involved in metanephros morphogenesis|mesonephros development|metanephric collecting duct development|metanephric comma-shaped body morphogenesis|metanephric distal convoluted tubule development|metanephric nephron tubule formation|metanephric S-shaped body morphogenesis|negative regulation of mesenchymal stem cell apoptosis involved in metanephric nephron morphogenesis|otic vesicle development|positive regulation of branching involved in ureteric bud morphogenesis|positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis|positive regulation of metanephric DCT cell differentiation|positive regulation of thyroid hormone generation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|pronephric field specification|regulation of metanephric nephron tubule epithelial cell differentiation|regulation of thyroid-stimulating hormone secretion|thyroid gland development|transcription, DNA-dependent	nucleoplasm	protein binding|RNA polymerase II core promoter sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|thyroid-stimulating hormone receptor activity	g.chr2:114002079C>A	X69699	CCDS42735.1, CCDS42736.1, CCDS46398.1, CCDS46399.1	2q13	2011-06-20	2007-07-12		ENSG00000125618	ENSG00000125618		"""Paired boxes"", ""Homeoboxes / PRD class"""	8622	protein-coding gene	gene with protein product		167415	"""paired box gene 8"""			8431641, 7981748	Standard	NM_003466		Approved		uc010yxt.2	Q06710	OTTHUMG00000128529	ENST00000429538.3:c.314G>T	2.37:g.114002079C>A	ENSP00000395498:p.Trp105Leu					PAX8_ENST00000397647.3_Missense_Mutation_p.W105L|PAX8_ENST00000348715.5_Missense_Mutation_p.W105L|PAX8_ENST00000263334.5_Missense_Mutation_p.W105L|PAX8_ENST00000263335.7_Missense_Mutation_p.W105L|AC016683.6_ENST00000556070.1_RNA|AC016683.6_ENST00000553869.2_RNA|AC016683.6_ENST00000422956.1_RNA|AC016683.6_ENST00000333145.5_RNA|AC016683.6_ENST00000436293.2_RNA|AC016683.6_ENST00000451179.1_RNA|AC016683.6_ENST00000445745.1_RNA	p.W105L	NM_003466.3	NP_003457.1	Q06710	PAX8_HUMAN			4	508	-			105			Paired.		Q09155|Q16337|Q16338|Q16339|Q4ZG35|Q96J49	Missense_Mutation	SNP	ENST00000429538.3	37	c.314G>T	CCDS46398.1	.	.	.	.	.	.	.	.	.	.	C	28.7	4.940629	0.92526	.	.	ENSG00000125618	ENST00000263335;ENST00000397647;ENST00000348715;ENST00000429538;ENST00000263334	D;D;D;D;D	0.99677	-6.37;-6.37;-6.37;-6.37;-6.37	5.32	5.32	0.75619	Paired box protein, N-terminal (3);Winged helix-turn-helix transcription repressor DNA-binding (1);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.99840	0.9927	H	0.97365	3.99	0.80722	D	1	D;D;D;D;D	0.89917	0.977;1.0;0.999;1.0;1.0	D;D;D;D;D	0.97110	0.923;0.999;0.994;0.996;1.0	D	0.96694	0.9513	10	0.87932	D	0	.	16.4863	0.84184	0.0:1.0:0.0:0.0	.	105;105;105;105;105	Q06710-2;Q06710-3;Q06710;Q06710-5;Q06710-4	.;.;PAX8_HUMAN;.;.	L	105	ENSP00000263335:W105L;ENSP00000380768:W105L;ENSP00000314750:W105L;ENSP00000395498:W105L;ENSP00000263334:W105L	ENSP00000263334:W105L	W	-	2	0	PAX8	113718549	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.502000	0.84385	0.655000	0.94253	TGG		0.582	PAX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250353.5			8	252	1	0	0.000274275	1	0.000285246	8	252				
FOLR2	2350	broad.mit.edu	37	11	71932697	71932697	+	Missense_Mutation	SNP	C	C	T	rs140546240	byFrequency	TCGA-EM-A4FH-01A-11D-A257-08	TCGA-EM-A4FH-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ad41f60-e79a-4db3-9c26-8e74cf80c34c	c93a2e43-26fb-461a-a9ab-60b52d591e61	g.chr11:71932697C>T	ENST00000298223.6	+	5	846	c.659C>T	c.(658-660)gCg>gTg	p.A220V	FOLR2_ENST00000454954.2_Missense_Mutation_p.A179V|FOLR2_ENST00000449475.2_Missense_Mutation_p.A216V	NM_000803.4|NM_001113534.1|NM_001113535.1|NM_001113536.1	NP_000794.3|NP_001107006.1|NP_001107007.1|NP_001107008.1	P14207	FOLR2_HUMAN	folate receptor 2 (fetal)	220					folic acid transport (GO:0015884)	anchored component of external side of plasma membrane (GO:0031362)|extracellular region (GO:0005576)|membrane (GO:0016020)	folic acid binding (GO:0005542)|folic acid transporter activity (GO:0008517)			breast(3)|large_intestine(3)|ovary(1)|skin(1)	8					Folic Acid(DB00158)	GAGGAAGTGGCGAGGTTCTAT	0.577													C|||	3	0.000599042	0.0	0.0014	5008	,	,		20317	0.0		0.002	False		,,,				2504	0.0					ENST00000449475.2																			0				breast(3)|large_intestine(3)|ovary(1)|skin(1)	8						c.(646-648)gCg>gTg		folate receptor 2 (fetal)	Folic Acid(DB00158)	C	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	0,4400		0,0,2200	94.0	92.0	93.0		659,659,659,659	2.7	0.6	11	dbSNP_134	93	2,8584	2.2+/-6.3	0,2,4291	yes	missense,missense,missense,missense	FOLR2	NM_000803.4,NM_001113534.1,NM_001113535.1,NM_001113536.1	64,64,64,64	0,2,6491	TT,TC,CC		0.0233,0.0,0.0154	benign,benign,benign,benign	220/256,220/256,220/256,220/256	71932697	2,12984	2200	4293	6493	SO:0001583	missense	2350				folic acid transport	anchored to membrane|extracellular region|membrane fraction|plasma membrane	folic acid binding|receptor activity	g.chr11:71932697C>T	AK222539	CCDS8212.1	11q13.3-q14.1	2010-04-08			ENSG00000165457	ENSG00000165457			3793	protein-coding gene	gene with protein product		136425				1133088, 7698003	Standard	NM_000803		Approved		uc009ytf.3	P14207	OTTHUMG00000150394	ENST00000298223.6:c.659C>T	11.37:g.71932697C>T	ENSP00000298223:p.Ala220Val					FOLR2_ENST00000454954.2_Missense_Mutation_p.A179V|FOLR2_ENST00000298223.6_Missense_Mutation_p.A220V	p.A216V			P14207	FOLR2_HUMAN			5	945	+			220					Q05CA5|Q6GTE8	Missense_Mutation	SNP	ENST00000298223.6	37	c.647C>T	CCDS8212.1	2|2	9.157509157509158E-4|9.157509157509158E-4	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	2|2	0.002638522427440633|0.002638522427440633	c|c	14.45|14.45	2.540069|2.540069	0.45176|0.45176	0.0|0.0	2.33E-4|2.33E-4	ENSG00000165457|ENSG00000165457	ENST00000449475;ENST00000298223;ENST00000454954|ENST00000413873	D;T;D|.	0.83837|.	-1.51;-1.25;-1.77|.	4.58|4.58	2.69|2.69	0.31865|0.31865	.|.	0.137686|.	0.47852|.	N|.	0.000201|.	T|.	0.55784|.	0.1942|.	M|M	0.76002|0.76002	2.32|2.32	0.48236|0.48236	D|D	0.999616|0.999616	P|.	0.50528|.	0.936|.	P|.	0.44946|.	0.465|.	T|.	0.52426|.	-0.8577|.	10|.	0.59425|0.02654	D|T	0.04|1	.|.	8.6922|8.6922	0.34273|0.34273	0.0:0.8097:0.0:0.1903|0.0:0.8097:0.0:0.1903	.|.	220|.	P14207|.	FOLR2_HUMAN|.	V|X	216;220;179|234	ENSP00000405638:A216V;ENSP00000298223:A220V;ENSP00000414094:A179V|.	ENSP00000298223:A220V|ENSP00000412980:R234X	A|R	+|+	2|1	0|2	FOLR2|FOLR2	71610345|71610345	0.994000|0.994000	0.37717|0.37717	0.571000|0.571000	0.28486|0.28486	0.584000|0.584000	0.36387|0.36387	3.173000|3.173000	0.50839|0.50839	0.545000|0.545000	0.28902|0.28902	0.462000|0.462000	0.41574|0.41574	GCG|CGA		0.577	FOLR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317923.2	NM_000803		29	41	0	0	0	1	0	29	41				
EFCAB14	9813	broad.mit.edu	37	1	47144235	47144235	+	Silent	SNP	G	G	A			TCGA-EM-A4FH-01A-11D-A257-08	TCGA-EM-A4FH-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ad41f60-e79a-4db3-9c26-8e74cf80c34c	c93a2e43-26fb-461a-a9ab-60b52d591e61	g.chr1:47144235G>A	ENST00000371933.3	-	11	2362	c.1386C>T	c.(1384-1386)tcC>tcT	p.S462S	EFCAB14_ENST00000544071.1_Intron|EFCAB14-AS1_ENST00000442839.1_RNA|EFCAB14-AS1_ENST00000418985.1_RNA	NM_014774.2	NP_055589.1	O75071	EFC14_HUMAN	EF-hand calcium binding domain 14	462	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.						calcium ion binding (GO:0005509)										CAGAACCTAGGGAGGTCCAGA	0.453																																						ENST00000371933.3																			0											c.(1384-1386)tcC>tcT		EF-hand calcium binding domain 14							100.0	99.0	99.0					1																	47144235		2203	4300	6503	SO:0001819	synonymous_variant	9813							g.chr1:47144235G>A	AB007963	CCDS30706.1	1p33	2013-01-10	2012-11-29	2012-11-29	ENSG00000159658	ENSG00000159658		"""EF-hand domain containing"""	29051	protein-coding gene	gene with protein product			"""KIAA0494"""	KIAA0494		9455484	Standard	NM_014774		Approved		uc001cqk.4	O75071	OTTHUMG00000007992	ENST00000371933.3:c.1386C>T	1.37:g.47144235G>A						EFCAB14_ENST00000544071.1_Intron|EFCAB14-AS1_ENST00000442839.1_RNA|EFCAB14-AS1_ENST00000418985.1_RNA	p.S462S	NM_014774.2	NP_055589.1					11	2362	-								D3DQ23|Q5SXB8	Silent	SNP	ENST00000371933.3	37	c.1386C>T	CCDS30706.1																																																																																				0.453	EFCAB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021931.1	NM_014774		17	42	0	0	0	1	0	17	42				
PPP1R7	5510	broad.mit.edu	37	2	242089953	242089953	+	Missense_Mutation	SNP	A	A	G	rs554905687		TCGA-EM-A4FH-01A-11D-A257-08	TCGA-EM-A4FH-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ad41f60-e79a-4db3-9c26-8e74cf80c34c	c93a2e43-26fb-461a-a9ab-60b52d591e61	g.chr2:242089953A>G	ENST00000234038.6	+	1	517	c.43A>G	c.(43-45)Atg>Gtg	p.M15V	PPP1R7_ENST00000406106.3_Missense_Mutation_p.M15V|PASK_ENST00000405260.1_5'Flank|PASK_ENST00000403638.3_5'Flank|PPP1R7_ENST00000404405.3_Missense_Mutation_p.M15V|PPP1R7_ENST00000401987.1_Missense_Mutation_p.M15V|PASK_ENST00000358649.4_5'Flank|PPP1R7_ENST00000272983.8_Missense_Mutation_p.M15V|PASK_ENST00000539818.1_5'Flank|PASK_ENST00000234040.4_5'Flank|PPP1R7_ENST00000407025.1_Missense_Mutation_p.M15V|PPP1R7_ENST00000402734.1_Intron	NM_001282412.1|NM_001282413.1|NM_002712.1	NP_001269341.1|NP_001269342.1|NP_002703.1	Q15435	PP1R7_HUMAN	protein phosphatase 1, regulatory subunit 7	15					positive regulation of protein dephosphorylation (GO:0035307)|regulation of catalytic activity (GO:0050790)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	enzyme regulator activity (GO:0030234)|protein phosphatase type 1 regulator activity (GO:0008599)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|ovary(3)	23		all_cancers(19;6.1e-33)|all_epithelial(40;1.07e-13)|Breast(86;0.000141)|Renal(207;0.00528)|all_lung(227;0.0446)|Ovarian(221;0.104)|Lung NSC(271;0.115)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;6.92e-32)|all cancers(36;5.35e-29)|OV - Ovarian serous cystadenocarcinoma(60;3.4e-14)|Kidney(56;4.23e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.24e-08)|BRCA - Breast invasive adenocarcinoma(100;3.56e-06)|Lung(119;0.000588)|LUSC - Lung squamous cell carcinoma(224;0.0048)|Colorectal(34;0.0137)|COAD - Colon adenocarcinoma(134;0.096)		GTCGCAGGAGATGATGGAGGG	0.697													A|||	1	0.000199681	0.0	0.0	5008	,	,		11776	0.0		0.0	False		,,,				2504	0.001				NSCLC(62;446 1299 5417 11238 27640)	ENST00000234038.6																			0				cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|ovary(3)	23						c.(43-45)Atg>Gtg		protein phosphatase 1, regulatory subunit 7							15.0	19.0	18.0					2																	242089953		2185	4283	6468	SO:0001583	missense	5510					cytoplasm|nucleus	protein binding|protein phosphatase type 1 regulator activity	g.chr2:242089953A>G	AF067136	CCDS2546.1, CCDS63190.1, CCDS63192.1, CCDS63193.1, CCDS63194.1	2q37.3	2012-04-17	2011-10-04		ENSG00000115685	ENSG00000115685		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	9295	protein-coding gene	gene with protein product		602877	"""protein phosphatase 1, regulatory (inhibitor) subunit 7"""			7498485, 7670491, 10231361	Standard	NM_001282413		Approved	sds22	uc002wat.1	Q15435	OTTHUMG00000133390	ENST00000234038.6:c.43A>G	2.37:g.242089953A>G	ENSP00000234038:p.Met15Val					PPP1R7_ENST00000404405.3_Missense_Mutation_p.M15V|PPP1R7_ENST00000402734.1_Intron|PPP1R7_ENST00000401987.1_Missense_Mutation_p.M15V|PPP1R7_ENST00000272983.8_Missense_Mutation_p.M15V|PPP1R7_ENST00000407025.1_Missense_Mutation_p.M15V|PPP1R7_ENST00000406106.3_Missense_Mutation_p.M15V	p.M15V	NM_002712.1	NP_002703.1	Q15435	PP1R7_HUMAN		Epithelial(32;6.92e-32)|all cancers(36;5.35e-29)|OV - Ovarian serous cystadenocarcinoma(60;3.4e-14)|Kidney(56;4.23e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.24e-08)|BRCA - Breast invasive adenocarcinoma(100;3.56e-06)|Lung(119;0.000588)|LUSC - Lung squamous cell carcinoma(224;0.0048)|Colorectal(34;0.0137)|COAD - Colon adenocarcinoma(134;0.096)	1	517	+		all_cancers(19;6.1e-33)|all_epithelial(40;1.07e-13)|Breast(86;0.000141)|Renal(207;0.00528)|all_lung(227;0.0446)|Ovarian(221;0.104)|Lung NSC(271;0.115)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238)	15					B4DFD4|B5MCY6|Q9UQE5|Q9UQE6|Q9Y6K4	Missense_Mutation	SNP	ENST00000234038.6	37	c.43A>G	CCDS2546.1	.	.	.	.	.	.	.	.	.	.	A	16.10	3.026008	0.54683	.	.	ENSG00000115685	ENST00000407025;ENST00000272983;ENST00000234038;ENST00000404405;ENST00000439916;ENST00000406106;ENST00000401987	T;T;T;T;T;T;T	0.46063	0.88;1.02;0.88;1.02;1.28;1.19;1.1	4.51	4.51	0.55191	.	0.253028	0.34700	N	0.003743	T	0.39937	0.1097	N	0.08118	0	0.35590	D	0.807017	B;P;P;P	0.43578	0.452;0.713;0.811;0.713	P;P;P;P	0.57846	0.455;0.678;0.828;0.678	T	0.56673	-0.7940	10	0.54805	T	0.06	-29.2562	12.4082	0.55451	1.0:0.0:0.0:0.0	.	15;15;15;15	Q15435-2;Q15435;Q15435-3;B5MBZ8	.;PP1R7_HUMAN;.;.	V	15	ENSP00000385657:M15V;ENSP00000272983:M15V;ENSP00000234038:M15V;ENSP00000385498:M15V;ENSP00000409719:M15V;ENSP00000385022:M15V;ENSP00000385466:M15V	ENSP00000234038:M15V	M	+	1	0	PPP1R7	241738626	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.301000	0.65727	1.674000	0.50907	0.402000	0.26972	ATG		0.697	PPP1R7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257244.4	NM_002712		3	25	0	0	0	1	0	3	25				
TXNDC2	84203	broad.mit.edu	37	18	9886894	9886894	+	Missense_Mutation	SNP	A	A	G			TCGA-EM-A4FH-01A-11D-A257-08	TCGA-EM-A4FH-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ad41f60-e79a-4db3-9c26-8e74cf80c34c	c93a2e43-26fb-461a-a9ab-60b52d591e61	g.chr18:9886894A>G	ENST00000306084.6	+	2	617	c.418A>G	c.(418-420)Aaa>Gaa	p.K140E	TXNDC2_ENST00000357775.5_Missense_Mutation_p.K73E|TXNDC2_ENST00000536353.2_Missense_Mutation_p.K73E|TXNDC2_ENST00000426718.3_3'UTR	NM_001098529.1	NP_001091999.1	Q86VQ3	TXND2_HUMAN	thioredoxin domain containing 2 (spermatozoa)	140	22 X 15 AA approximate tandem repeat of Q-P-K-X-G-D-I-P-K-S-[PS]-E-[KE]-X-I.				cell differentiation (GO:0030154)|cell redox homeostasis (GO:0045454)|glycerol ether metabolic process (GO:0006662)|multicellular organismal development (GO:0007275)|oxidation-reduction process (GO:0055114)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|motile cilium (GO:0031514)|nucleolus (GO:0005730)|nucleus (GO:0005634)|outer dense fiber (GO:0001520)	nutrient reservoir activity (GO:0045735)|protein disulfide isomerase activity (GO:0003756)|protein disulfide oxidoreductase activity (GO:0015035)|thioredoxin-disulfide reductase activity (GO:0004791)	p.K140E(2)|p.K73E(2)		NS(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|skin(7)|urinary_tract(1)	31						GTCCTCAGAAAAAGCCATCCA	0.547																																						ENST00000306084.6																			4	Substitution - Missense(4)	p.K140E(2)|p.K73E(2)	urinary_tract(2)|lung(2)	NS(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|skin(7)|urinary_tract(1)	31						c.(418-420)Aaa>Gaa		thioredoxin domain containing 2 (spermatozoa)							133.0	131.0	132.0					18																	9886894		2203	4300	6503	SO:0001583	missense	0				cell differentiation|cell redox homeostasis|glycerol ether metabolic process|multicellular organismal development|spermatogenesis	cytoplasm	electron carrier activity|nutrient reservoir activity|protein disulfide oxidoreductase activity|thioredoxin-disulfide reductase activity	g.chr18:9886894A>G	AF080095	CCDS11846.1, CCDS42414.1	18p11.31-p11.2	2009-03-11	2009-03-11	2007-08-16	ENSG00000168454	ENSG00000168454			16470	protein-coding gene	gene with protein product	"""sperm-specific thioredoxin 1"""					11230166, 11399755	Standard	NM_001098529		Approved	SPTRX1	uc002koi.4	Q86VQ3	OTTHUMG00000131602	ENST00000306084.6:c.418A>G	18.37:g.9886894A>G	ENSP00000304908:p.Lys140Glu					TXNDC2_ENST00000357775.4_Missense_Mutation_p.K73E|TXNDC2_ENST00000426718.3_3'UTR|TXNDC2_ENST00000584255.1_3'UTR|TXNDC2_ENST00000536353.2_Missense_Mutation_p.K73E	p.K140E	NM_001098529.1	NP_001091999.1	Q86VQ3	TXND2_HUMAN			2	617	+			140			22 X 15 AA approximate tandem repeat of Q-P-K-X-G-D-I-P-K-S-[PS]-E-[KE]-X-I.		A5YM73|Q8N7U4|Q96RX3|Q9H0L8	Missense_Mutation	SNP	ENST00000306084.6	37	c.418A>G	CCDS42414.1	.	.	.	.	.	.	.	.	.	.	a	8.625	0.892206	0.17613	.	.	ENSG00000168454	ENST00000536353;ENST00000357775;ENST00000306084;ENST00000426718	T;T;T	0.20069	2.1;2.3;2.3	3.48	-6.96	0.01622	.	1.199930	0.06365	N	0.712409	T	0.12774	0.0310	L	0.35854	1.095	0.09310	N	1	B	0.25048	0.117	B	0.25884	0.064	T	0.32693	-0.9897	9	.	.	.	.	5.8007	0.18412	0.5013:0.2415:0.2572:0.0	.	140	Q86VQ3	TXND2_HUMAN	E	73;73;140;140	ENSP00000437393:K73E;ENSP00000350419:K73E;ENSP00000304908:K140E	.	K	+	1	0	TXNDC2	9876894	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.892000	0.04131	-1.042000	0.03262	-1.380000	0.01176	AAA		0.547	TXNDC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254487.1			4	138	0	0	0	1	0	4	138				
ALMS1	7840	broad.mit.edu	37	2	73677492	73677492	+	Missense_Mutation	SNP	G	G	A			TCGA-EM-A4FH-01A-11D-A257-08	TCGA-EM-A4FH-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ad41f60-e79a-4db3-9c26-8e74cf80c34c	c93a2e43-26fb-461a-a9ab-60b52d591e61	g.chr2:73677492G>A	ENST00000264448.6	+	8	3946	c.3835G>A	c.(3835-3837)Gct>Act	p.A1279T	ALMS1_ENST00000377715.1_Missense_Mutation_p.A1279T|ALMS1_ENST00000409009.1_Missense_Mutation_p.A1237T	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	1279	34 X 47 AA approximate tandem repeat.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)		p.A1279T(1)		breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						TGGCACACCAGCTGTAACCTC	0.433																																						ENST00000264448.6																			1	Substitution - Missense(1)	p.A1279T(1)	urinary_tract(1)	breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						c.(3835-3837)Gct>Act		Alstrom syndrome 1							87.0	89.0	88.0					2																	73677492		1835	4091	5926	SO:0001583	missense	7840				G2/M transition of mitotic cell cycle	centrosome|cilium|cytosol|microtubule basal body|spindle pole		g.chr2:73677492G>A	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.3835G>A	2.37:g.73677492G>A	ENSP00000264448:p.Ala1279Thr					ALMS1_ENST00000409009.1_Missense_Mutation_p.A1237T|ALMS1_ENST00000377715.1_Missense_Mutation_p.A1279T	p.A1279T	NM_015120.4	NP_055935.4	Q8TCU4	ALMS1_HUMAN			8	3946	+			1279			34 X 47 AA approximate tandem repeat.		Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	37	c.3835G>A	CCDS42697.1	.	.	.	.	.	.	.	.	.	.	G	0.138	-1.105576	0.01828	.	.	ENSG00000116127	ENST00000409009;ENST00000264448;ENST00000377715	T;T;T	0.14893	3.37;3.37;2.47	4.44	-8.87	0.00792	.	.	.	.	.	T	0.02970	0.0088	N	0.01668	-0.77	0.09310	N	1	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.27365	-1.0076	9	0.06757	T	0.87	.	0.6373	0.00804	0.1908:0.2119:0.2851:0.3122	.	1279;1237;1279	Q8TCU4-3;B8ZZJ3;Q8TCU4	.;.;ALMS1_HUMAN	T	1237;1279;1279	ENSP00000386627:A1237T;ENSP00000264448:A1279T;ENSP00000366944:A1279T	ENSP00000264448:A1279T	A	+	1	0	ALMS1	73531000	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.877000	0.00344	-2.395000	0.00582	-1.298000	0.01336	GCT		0.433	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		4	123	0	0	0	1	0	4	123				
PADI6	353238	broad.mit.edu	37	1	17721722	17721723	+	RNA	DEL	GA	GA	-	rs147310450|rs141096512|rs58784721	byFrequency	TCGA-EM-A4FH-01A-11D-A257-08	TCGA-EM-A4FH-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ad41f60-e79a-4db3-9c26-8e74cf80c34c	c93a2e43-26fb-461a-a9ab-60b52d591e61	g.chr1:17721722_17721723delGA	ENST00000434762.2	+	0	1545							Q6TGC4	PADI6_HUMAN	peptidyl arginine deiminase, type VI						cytoplasm organization (GO:0007028)|cytoskeleton organization (GO:0007010)|protein citrullination (GO:0018101)|regulation of translation by machinery localization (GO:0043143)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(2)	29		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00488)|BRCA - Breast invasive adenocarcinoma(304;7.59e-06)|COAD - Colon adenocarcinoma(227;1.18e-05)|Kidney(64;0.000186)|KIRC - Kidney renal clear cell carcinoma(64;0.00272)|STAD - Stomach adenocarcinoma(196;0.0134)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.189)	L-Citrulline(DB00155)	tttgttttttgagagtcttgct	0.485														1607	0.320887	0.3389	0.366	5008	,	,		16526	0.1716		0.3738	False		,,,				2504	0.364					ENST00000434762.2																			0				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(2)	29								peptidyl arginine deiminase, type VI	L-Citrulline(DB00155)																																					353238				peptidyl-citrulline biosynthetic process from peptidyl-arginine	cytoplasm|nucleus	calcium ion binding|protein-arginine deiminase activity	g.chr1:17721722_17721723delGA	AY422079	CCDS72715.1	1p36.13	2014-07-10			ENSG00000256049	ENSG00000276747	3.5.3.15	"""Peptidyl arginine deiminases"""	20449	protein-coding gene	gene with protein product		610363				15087120	Standard	NM_207421		Approved		uc001bak.1	Q6TGC4	OTTHUMG00000002372		1.37:g.17721724_17721725delGA										Q6TGC4	PADI6_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.00488)|BRCA - Breast invasive adenocarcinoma(304;7.59e-06)|COAD - Colon adenocarcinoma(227;1.18e-05)|Kidney(64;0.000186)|KIRC - Kidney renal clear cell carcinoma(64;0.00272)|STAD - Stomach adenocarcinoma(196;0.0134)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.189)	0	1545	+		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)						Q330K5|Q70SX3	RNA	DEL	ENST00000434762.2	37																																																																																						0.485	PADI6-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000006804.4	NM_207421		4	6						4	6	---	---	---	---
MACF1	23499	broad.mit.edu	37	1	39799059	39799060	+	Frame_Shift_Ins	INS	-	-	G			TCGA-EM-A4FH-01A-11D-A257-08	TCGA-EM-A4FH-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ad41f60-e79a-4db3-9c26-8e74cf80c34c	c93a2e43-26fb-461a-a9ab-60b52d591e61	g.chr1:39799059_39799060insG	ENST00000372915.3	+	36	6901_6902	c.6814_6815insG	c.(6814-6816)aggfs	p.R2272fs	MACF1_ENST00000361689.2_Intron|MACF1_ENST00000545844.1_Intron|MACF1_ENST00000567887.1_Frame_Shift_Ins_p.R2304fs|MACF1_ENST00000476350.1_Intron|MACF1_ENST00000289893.4_Frame_Shift_Ins_p.R707fs|MACF1_ENST00000564288.1_Frame_Shift_Ins_p.R2267fs|MACF1_ENST00000317713.7_Intron|MACF1_ENST00000539005.1_Intron			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	2272					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			AGATAGTGGCAGGGAAATTTTT	0.391																																						ENST00000564288.1																			0				breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203						c.(6799-6801)ggafs		microtubule-actin crosslinking factor 1																																				SO:0001589	frameshift_variant	23499				cell cycle arrest|Golgi to plasma membrane protein transport|positive regulation of Wnt receptor signaling pathway|regulation of epithelial cell migration|regulation of focal adhesion assembly|regulation of microtubule-based process|Wnt receptor signaling pathway|wound healing	Golgi apparatus|microtubule|ruffle membrane	actin filament binding|ATPase activity|calcium ion binding|microtubule binding	g.chr1:39799059_39799060insG	AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"""EF-hand domain containing"""	13664	protein-coding gene	gene with protein product	"""actin cross-linking factor"", ""620 kDa actin binding protein"", ""macrophin 1"", ""trabeculin-alpha"", ""actin cross-linking family protein 7"""	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.6817dupG	1.37:g.39799062_39799062dupG	ENSP00000362006:p.Arg2272fs					MACF1_ENST00000317713.7_Intron|MACF1_ENST00000372915.3_Frame_Shift_Ins_p.G2272fs|MACF1_ENST00000289893.4_Frame_Shift_Ins_p.G707fs|MACF1_ENST00000567887.1_Frame_Shift_Ins_p.G2304fs|MACF1_ENST00000476350.1_Intron|MACF1_ENST00000539005.1_Intron|MACF1_ENST00000545844.1_Intron|MACF1_ENST00000361689.2_Intron	p.G2267fs			Q9UPN3	MACF1_HUMAN	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)		37	7576_7577	+	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	2272					B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Frame_Shift_Ins	INS	ENST00000372915.3	37	c.6799_6800insG																																																																																					0.391	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		19	56						19	56	---	---	---	---
LOC101927237	101927237	broad.mit.edu	37	4	68311813	68311814	+	lincRNA	INS	-	-	ACCGCCACCGCC	rs11267830|rs141262603|rs373609666|rs112837692	byFrequency	TCGA-EM-A4FH-01A-11D-A257-08	TCGA-EM-A4FH-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ad41f60-e79a-4db3-9c26-8e74cf80c34c	c93a2e43-26fb-461a-a9ab-60b52d591e61	g.chr4:68311813_68311814insACCGCCACCGCC	ENST00000502400.1	-	0	34																											ccgctaccgctaccgccaccgc	0.639														3662	0.73123	0.5696	0.8012	5008	,	,		12072	0.7927		0.7684	False		,,,				2504	0.7986					ENST00000502400.1																			0																																																			0							g.chr4:68311813_68311814insACCGCCACCGCC																													4.37:g.68311813_68311814insACCGCCACCGCC														0	34	-									RNA	INS	ENST00000502400.1	37																																																																																						0.639	RP11-584P21.2-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000361926.2			4	3						4	3	---	---	---	---
HLA-DRB6	3128	broad.mit.edu	37	6	32523362	32523363	+	RNA	INS	-	-	GATA	rs142676080|rs190692498		TCGA-EM-A4FH-01A-11D-A257-08	TCGA-EM-A4FH-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ad41f60-e79a-4db3-9c26-8e74cf80c34c	c93a2e43-26fb-461a-a9ab-60b52d591e61	g.chr6:32523362_32523363insGATA	ENST00000411500.1	-	0	458					NR_001298.1				major histocompatibility complex, class II, DR beta 6 (pseudogene)																		AAAGCAATGTGGATAAAGGGAC	0.431																																						ENST00000411500.1																			0																																																			0							g.chr6:32523362_32523363insGATA	L76566		6p21.3	2011-07-08			ENSG00000229391	ENSG00000229391		"""Histocompatibility complex"""	4954	pseudogene	pseudogene						1529427, 10436177	Standard	NR_001298		Approved		uc003obn.1		OTTHUMG00000031028		6.37:g.32523363_32523366dupGATA								NR_001298.1						0	458	-									RNA	INS	ENST00000411500.1	37																																																																																						0.431	HLA-DRB6-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000272900.1	NR_001298		4	5						4	5	---	---	---	---
MUC3A	4584	broad.mit.edu	37	7	100609618	100609619	+	Frame_Shift_Ins	INS	-	-	T			TCGA-EM-A4FH-01A-11D-A257-08	TCGA-EM-A4FH-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ad41f60-e79a-4db3-9c26-8e74cf80c34c	c93a2e43-26fb-461a-a9ab-60b52d591e61	g.chr7:100609618_100609619insT	ENST00000319509.7	+	8	2350_2351	c.2350_2351insT	c.(2350-2352)ctgfs	p.L784fs	RP11-395B7.2_ENST00000420080.1_RNA|RP11-395B7.2_ENST00000434775.1_RNA			Q02505	MUC3A_HUMAN	mucin 3A, cell surface associated	2449	Ser-rich.|Thr-rich.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|extracellular matrix structural constituent (GO:0005201)			breast(3)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(1)|lung(32)|prostate(3)	44						GGTCGGGGGCCTGACGGCCGGC	0.757																																						ENST00000319509.7																			0				breast(3)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(1)|lung(32)|prostate(3)	44						c.(2350-2352)gacfs		mucin 3A, cell surface associated																																				SO:0001589	frameshift_variant	4584							g.chr7:100609618_100609619insT	AF113616		7q22.1	2012-04-20	2006-03-14		ENSG00000169894	ENSG00000169894		"""Mucins"""	7513	protein-coding gene	gene with protein product		158371	"""mucin 3A, intestinal"""	MUC3		2393399, 10973822	Standard	XM_006710192		Approved		uc003uxl.1	Q02505	OTTHUMG00000157038	ENST00000319509.7:c.2351dupT	7.37:g.100609619_100609619dupT	ENSP00000324834:p.Leu784fs					RP11-395B7.2_ENST00000420080.1_RNA	p.D784fs							8	2350_2351	+								O14650|O14651|O43418|O43421|Q02506|Q6W763|Q9H3Q7|Q9UKW9|Q9UN93|Q9UN94|Q9UN95	Frame_Shift_Ins	INS	ENST00000319509.7	37	c.2350_2351insT																																																																																					0.757	MUC3A-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000347215.1	XM_001725354		5	10						5	10	---	---	---	---
LTBP3	4054	broad.mit.edu	37	11	65318671	65318671	+	Frame_Shift_Del	DEL	G	G	-			TCGA-EM-A4FH-01A-11D-A257-08	TCGA-EM-A4FH-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ad41f60-e79a-4db3-9c26-8e74cf80c34c	c93a2e43-26fb-461a-a9ab-60b52d591e61	g.chr11:65318671delG	ENST00000301873.5	-	11	1914	c.1646delC	c.(1645-1647)ccgfs	p.P549fs	LTBP3_ENST00000532932.1_5'Flank|LTBP3_ENST00000536982.1_Frame_Shift_Del_p.P175fs|LTBP3_ENST00000322147.4_Frame_Shift_Del_p.P549fs	NM_001130144.2	NP_001123616.1	Q9NS15	LTBP3_HUMAN	latent transforming growth factor beta binding protein 3	549					bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|extracellular matrix organization (GO:0030198)|lung saccule development (GO:0060430)|negative regulation of bone mineralization (GO:0030502)|negative regulation of chondrocyte differentiation (GO:0032331)|positive regulation of bone resorption (GO:0045780)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of mesenchymal stem cell proliferation (GO:1902462)|transforming growth factor beta activation (GO:0036363)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|prostate(2)|upper_aerodigestive_tract(3)	23						GCGCATGGTCGGGGGCGAGGG	0.647																																						ENST00000301873.5																			0				breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|prostate(2)|upper_aerodigestive_tract(3)	23						c.(1645-1647)cgfs		latent transforming growth factor beta binding protein 3							31.0	20.0	23.0					11																	65318671		2146	4199	6345	SO:0001589	frameshift_variant	4054					extracellular region	calcium ion binding|growth factor binding	g.chr11:65318671delG	AF135960	CCDS8103.1, CCDS44647.1	11q12	2011-10-20			ENSG00000168056	ENSG00000168056		"""Latent transforming growth factor, beta binding proteins"""	6716	protein-coding gene	gene with protein product		602090		LTBP2		7719025	Standard	NM_001164266		Approved		uc001oej.3	Q9NS15	OTTHUMG00000166575	ENST00000301873.5:c.1646delC	11.37:g.65318671delG	ENSP00000301873:p.Pro549fs					LTBP3_ENST00000536982.1_Frame_Shift_Del_p.P175fs|LTBP3_ENST00000322147.4_Frame_Shift_Del_p.P549fs	p.P549fs	NM_001130144.2	NP_001123616.1	Q9NS15	LTBP3_HUMAN			11	1914	-			549					O15107|Q96HB9|Q9H7K2|Q9UFN4	Frame_Shift_Del	DEL	ENST00000301873.5	37	c.1646delC	CCDS44647.1																																																																																				0.647	LTBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390538.1	NM_021070		2	4						2	4	---	---	---	---
OVOS2	144203	broad.mit.edu	37	12	31269189	31269190	+	RNA	INS	-	-	ATCAT	rs25559|rs10665556	byFrequency	TCGA-EM-A4FH-01A-11D-A257-08	TCGA-EM-A4FH-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ad41f60-e79a-4db3-9c26-8e74cf80c34c	c93a2e43-26fb-461a-a9ab-60b52d591e61	g.chr12:31269189_31269190insATCAT	ENST00000542490.1	-	0	165																				central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(25)|prostate(3)|stomach(3)|urinary_tract(1)	41						CATGAGAACTCATTACCATGAT	0.351														3178	0.634585	0.7088	0.611	5008	,	,		12379	0.8274		0.4284	False		,,,				2504	0.5644					ENST00000542490.1																			0				central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(25)|prostate(3)|stomach(3)|urinary_tract(1)	41																																														0							g.chr12:31269189_31269190insATCAT																													12.37:g.31269189_31269190insATCAT														0	165	-									RNA	INS	ENST00000542490.1	37																																																																																						0.351	RP11-551L14.1-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400342.1			2	4						2	4	---	---	---	---
TRAV9-2	28677	broad.mit.edu	37	14	22409533	22409539	+	RNA	DEL	CTCTCTC	CTCTCTC	-	rs374912343|rs371270332|rs2178778|rs587678559|rs201742006|rs367992314	byFrequency	TCGA-EM-A4FH-01A-11D-A257-08	TCGA-EM-A4FH-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ad41f60-e79a-4db3-9c26-8e74cf80c34c	c93a2e43-26fb-461a-a9ab-60b52d591e61	g.chr14:22409533_22409539delCTCTCTC	ENST00000390441.2	+	0	102									T cell receptor alpha variable 9-2																		ctctctctctctctctctTTTTTTTTT	0.415																																						ENST00000390441.2																			0																																																			0							g.chr14:22409533_22409539delCTCTCTC	AE000659		14q11.2	2012-02-07			ENSG00000211793	ENSG00000211793		"""T cell receptors / TRA locus"""	12154	other	T cell receptor gene						8188290	Standard	NG_001332		Approved				OTTHUMG00000170637		14.37:g.22409533_22409539delCTCTCTC														0	102	+									RNA	DEL	ENST00000390441.2	37																																																																																						0.415	TRAV9-2-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	TR_V_gene	TR_V_gene	OTTHUMT00000409885.1	NG_001332		4	4						4	4	---	---	---	---
RP5-991G20.1	0	broad.mit.edu	37	16	72763869	72763869	+	RNA	DEL	A	A	-			TCGA-EM-A4FH-01A-11D-A257-08	TCGA-EM-A4FH-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ad41f60-e79a-4db3-9c26-8e74cf80c34c	c93a2e43-26fb-461a-a9ab-60b52d591e61	g.chr16:72763869delA	ENST00000563328.2	+	0	164																											GGTCCAAAACAAAAAAAAAAA	0.433																																						ENST00000563328.2																			0																																																			0							g.chr16:72763869delA																													16.37:g.72763869delA														0	164	+									RNA	DEL	ENST00000563328.2	37																																																																																						0.433	RP5-991G20.1-001	KNOWN	basic	antisense	antisense	OTTHUMT00000421937.2			3	4						3	4	---	---	---	---
CCDC155	147872	broad.mit.edu	37	19	49920666	49920668	+	In_Frame_Del	DEL	CTG	CTG	-	rs139882972		TCGA-EM-A4FH-01A-11D-A257-08	TCGA-EM-A4FH-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ad41f60-e79a-4db3-9c26-8e74cf80c34c	c93a2e43-26fb-461a-a9ab-60b52d591e61	g.chr19:49920666_49920668delCTG	ENST00000447857.3	+	20	1793_1795	c.1588_1590delCTG	c.(1588-1590)ctgdel	p.L536del		NM_144688.4	NP_653289.3	Q8N6L0	KASH5_HUMAN	coiled-coil domain containing 155	536	Poly-Leu.					chromosome, telomeric region (GO:0000781)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(10)|ovary(1)|stomach(1)	22						TGTCCTGGGCctgctgctgctgc	0.65																																						ENST00000447857.3																			0				NS(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(10)|ovary(1)|stomach(1)	22						c.(1588-1590)del		coiled-coil domain containing 155				2,210,3744		1,0,0,70,70,1837						-4.5	0.9		dbSNP_134	52	8,291,7573		1,0,6,67,157,3705	no	codingComplex	CCDC155	NM_144688.4		2,0,6,137,227,5542	A1A1,A1A2,A1R,A2A2,A2R,RR		3.7983,5.3589,4.3203				10,501,11317				SO:0001651	inframe_deletion	147872					integral to membrane	calcium ion binding	g.chr19:49920666_49920668delCTG		CCDS46140.1	19q13.33	2014-01-21			ENSG00000161609	ENSG00000161609			26520	protein-coding gene	gene with protein product							Standard	NM_144688		Approved	FLJ32658, KASH5	uc002pnm.2	Q8N6L0	OTTHUMG00000183170	ENST00000447857.3:c.1588_1590delCTG	19.37:g.49920675_49920677delCTG	ENSP00000404220:p.Leu536del						p.L536del	NM_144688.4	NP_653289.3	Q8N6L0	CC155_HUMAN			20	1793_1795	+			536			Poly-Leu.		Q96MC3	In_Frame_Del	DEL	ENST00000447857.3	37	c.1588_1590delCTG	CCDS46140.1																																																																																				0.650	CCDC155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465436.2	NM_144688		3	5						3	5	---	---	---	---
CSF2RB	1439	broad.mit.edu	37	22	37333749	37333750	+	Frame_Shift_Ins	INS	-	-	G			TCGA-EM-A4FH-01A-11D-A257-08	TCGA-EM-A4FH-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ad41f60-e79a-4db3-9c26-8e74cf80c34c	c93a2e43-26fb-461a-a9ab-60b52d591e61	g.chr22:37333749_37333750insG	ENST00000403662.3	+	14	2121_2122	c.1899_1900insG	c.(1900-1902)gggfs	p.G634fs	CSF2RB_ENST00000262825.5_Frame_Shift_Ins_p.G640fs|CSF2RB_ENST00000536485.1_Frame_Shift_Ins_p.G581fs|CSF2RB_ENST00000406230.1_Frame_Shift_Ins_p.G640fs			P32927	IL3RB_HUMAN	colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage)	634					cellular response to interleukin-3 (GO:0036016)|interleukin-3-mediated signaling pathway (GO:0038156)|interleukin-5-mediated signaling pathway (GO:0038043)|respiratory gaseous exchange (GO:0007585)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)	granulocyte macrophage colony-stimulating factor receptor complex (GO:0030526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|receptor activity (GO:0004872)			breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(18)|ovary(3)|pancreas(1)|skin(5)|upper_aerodigestive_tract(2)	42					Sargramostim(DB00020)	GTCTGCCTGCTGGGGGGCAGGT	0.688																																						ENST00000262825.5																			0				breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(18)|ovary(3)|pancreas(1)|skin(5)|upper_aerodigestive_tract(2)	42						c.(1915-1920)gcggggfs		colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage)	Sargramostim(DB00020)																																			SO:0001589	frameshift_variant	1439				respiratory gaseous exchange	granulocyte macrophage colony-stimulating factor receptor complex	cytokine receptor activity	g.chr22:37333749_37333750insG	M59941	CCDS13936.1	22q12.3	2014-09-09			ENSG00000100368	ENSG00000100368		"""CD molecules"", ""Fibronectin type III domain containing"""	2436	protein-coding gene	gene with protein product		138981		IL3RB		1833064, 1424804	Standard	NM_000395		Approved	IL5RB, CD131	uc003aqa.4	P32927	OTTHUMG00000150546	ENST00000403662.3:c.1905dupG	22.37:g.37333755_37333755dupG	ENSP00000384053:p.Gly634fs					CSF2RB_ENST00000536485.1_Frame_Shift_Ins_p.AG580fs|CSF2RB_ENST00000406230.1_Frame_Shift_Ins_p.AG639fs|CSF2RB_ENST00000403662.3_Frame_Shift_Ins_p.AG633fs	p.AG639fs	NM_000395.2	NP_000386.1	P32927	IL3RB_HUMAN			14	2134_2135	+			633					Q5JZI1|Q6ICE0	Frame_Shift_Ins	INS	ENST00000403662.3	37	c.1917_1918insG	CCDS13936.1																																																																																				0.688	CSF2RB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318854.1	NM_000395		2	4						2	4	---	---	---	---
