#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
BTN2A3P	54718	broad.mit.edu	37	6	26422353	26422353	+	RNA	SNP	C	C	T	rs571530750	byFrequency	TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr6:26422353C>T	ENST00000466808.2	+	0	7							Q96KV6	BT2A3_HUMAN	butyrophilin, subfamily 2, member A3, pseudogene							integral component of membrane (GO:0016021)		p.P3S(2)									GCTCATGGAACCAGCTGCTGC	0.622													C|||	7	0.00139776	0.0023	0.0	5008	,	,		16376	0.001		0.0	False		,,,				2504	0.0031					ENST00000466808.2																			2	Substitution - Missense(2)	p.P3S(2)	endometrium(1)|kidney(1)																																																0							g.chr6:26422353C>T	AL021917		6p22.1	2014-01-14	2011-09-06	2011-09-06	ENSG00000124549	ENSG00000124549		"""Butyrophilins"""	13229	pseudogene	pseudogene		613592	"""butyrophilin, subfamily 2, member A3"""	BTN2A3			Standard	NR_027795		Approved	BTN2.3	uc011dkl.1	Q96KV6	OTTHUMG00000014453		6.37:g.26422353C>T														0	7	+								A6NEF4	RNA	SNP	ENST00000466808.2	37																																																																																						0.622	BTN2A3P-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000040118.4	NR_027795		11	603	0	0	0	1	0	11	603				
CYP4A11	1579	broad.mit.edu	37	1	47407091	47407091	+	Silent	SNP	C	C	G			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr1:47407091C>G	ENST00000310638.4	-	1	46	c.15G>C	c.(13-15)gtG>gtC	p.V5V	CYP4A11_ENST00000457840.2_5'UTR|CYP4A11_ENST00000462347.1_Silent_p.V5V|CYP4A11_ENST00000371905.1_Silent_p.V5V|CYP4A11_ENST00000371904.4_Silent_p.V5V	NM_000778.3	NP_000769.2	Q02928	CP4AB_HUMAN	cytochrome P450, family 4, subfamily A, polypeptide 11	5				V -> A (in Ref. 8; AA sequence). {ECO:0000305}.	arachidonic acid metabolic process (GO:0019369)|cellular lipid metabolic process (GO:0044255)|epoxygenase P450 pathway (GO:0019373)|fatty acid metabolic process (GO:0006631)|leukotriene B4 catabolic process (GO:0036101)|leukotriene metabolic process (GO:0006691)|long-chain fatty acid metabolic process (GO:0001676)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|positive regulation of icosanoid secretion (GO:0032305)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|arachidonic acid omega-hydroxylase activity (GO:0052869)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)			endometrium(2)|kidney(5)|large_intestine(6)|lung(6)|ovary(5)|prostate(3)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)	36					Cisplatin(DB00515)|Clofibrate(DB00636)|Dexamethasone(DB01234)|Estrone(DB00655)|Ethanol(DB00898)|Lansoprazole(DB00448)|Pegvisomant(DB00082)|Pentamidine(DB00738)|Phenobarbital(DB01174)|Rifampicin(DB01045)|Tretinoin(DB00755)	TGGGGCTCAGCACAGAGACAC	0.587																																						ENST00000310638.4																			0				endometrium(2)|kidney(5)|large_intestine(6)|lung(6)|ovary(5)|prostate(3)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)	36						c.(13-15)gtG>gtC		cytochrome P450, family 4, subfamily A, polypeptide 11	NADH(DB00157)						83.0	83.0	83.0					1																	47407091		2203	4300	6503	SO:0001819	synonymous_variant	1579				long-chain fatty acid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	alkane 1-monooxygenase activity|electron carrier activity|heme binding|oxygen binding	g.chr1:47407091C>G	L04751	CCDS543.1	1p33	2008-02-05	2003-01-14		ENSG00000187048	ENSG00000187048		"""Cytochrome P450s"""	2642	protein-coding gene	gene with protein product		601310	"""cytochrome P450, subfamily IVA, polypeptide 11"""	CYP4A2		7679927	Standard	NM_000778		Approved	CYP4AII	uc001cqp.4	Q02928	OTTHUMG00000008020	ENST00000310638.4:c.15G>C	1.37:g.47407091C>G						CYP4A11_ENST00000371905.1_Silent_p.V5V|CYP4A11_ENST00000475477.1_5'UTR|CYP4A11_ENST00000371904.4_Silent_p.V5V|CYP4A11_ENST00000457840.2_5'UTR	p.V5V	NM_000778.3	NP_000769.2	Q02928	CP4AB_HUMAN			1	46	-			5	V -> A (in Ref. 8; AA sequence).				Q06766|Q16865|Q16866|Q5VSP8|Q86SU6|Q8IWY5	Silent	SNP	ENST00000310638.4	37	c.15G>C	CCDS543.1																																																																																				0.587	CYP4A11-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022022.1	NM_000778		13	522	0	0	0	1	0	13	522				
KRTAP4-11	653240	broad.mit.edu	37	17	39274416	39274416	+	Missense_Mutation	SNP	C	C	T	rs408579	byFrequency	TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr17:39274416C>T	ENST00000391413.2	-	1	190	c.152G>A	c.(151-153)aGg>aAg	p.R51K		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	51	27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].		Missing (in allele KAP4.14). {ECO:0000269|PubMed:15955084}.			keratin filament (GO:0045095)		p.R51K(1)		endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(8)|prostate(5)|skin(1)	33		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			GCACTGGGGCCTGCAGCAGCT	0.672													t|||	242	0.0483227	0.1248	0.0202	5008	,	,		19066	0.005		0.0219	False		,,,				2504	0.0368					ENST00000391413.2																			1	Substitution - Missense(1)	p.R51K(1)	endometrium(1)	endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(8)|prostate(5)|skin(1)	33						c.(151-153)aGg>aAg		keratin associated protein 4-11							9.0	15.0	13.0					17																	39274416		682	1579	2261	SO:0001583	missense	653240					keratin filament		g.chr17:39274416C>T	AC025904	CCDS45675.1	17q21.2	2013-06-25			ENSG00000212721	ENSG00000212721		"""Keratin associated proteins"""	18911	protein-coding gene	gene with protein product			"""keratin associated protein 4-14"""	KRTAP4-14			Standard	NM_033059		Approved	KAP4.11, KAP4.14	uc002hvz.3	Q9BYQ6	OTTHUMG00000133586	ENST00000391413.2:c.152G>A	17.37:g.39274416C>T	ENSP00000375232:p.Arg51Lys						p.R51K	NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	STAD - Stomach adenocarcinoma(17;0.000371)		1	190	-		Breast(137;0.000496)	51		Missing (in allele KAP4.14).	27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].		A0AUY2	Missense_Mutation	SNP	ENST00000391413.2	37	c.152G>A	CCDS45675.1	.	.	.	.	.	.	.	.	.	.	.	4.205	0.036712	0.08148	.	.	ENSG00000212721	ENST00000391413	T	0.01455	4.87	3.47	-1.13	0.09775	.	2.855670	0.02563	U	0.096976	T	0.02610	0.0079	M	0.72118	2.19	0.09310	N	1	B	0.25441	0.126	B	0.28916	0.096	T	0.52283	-0.8596	10	0.05959	T	0.93	.	3.7627	0.08610	0.1684:0.4051:0.0:0.4265	rs408579	51	Q9BYQ6	KR411_HUMAN	K	51	ENSP00000375232:R51K	ENSP00000375232:R51K	R	-	2	0	KRTAP4-11	36527942	0.000000	0.05858	0.002000	0.10522	0.072000	0.16883	-0.738000	0.04871	-0.091000	0.12440	-0.208000	0.12717	AGG		0.672	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1			8	385	0	0	0	1	0	8	385				
TSSC2	650368	broad.mit.edu	37	11	3427845	3427845	+	RNA	SNP	C	C	T			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr11:3427845C>T	ENST00000529482.1	+	0	962									tumor suppressing subtransferable candidate 2 pseudogene																		CTTCAAGTGGCAGGAGCAGAA	0.587																																						ENST00000529482.1																			0																																																			0							g.chr11:3427845C>T			11p15.4	2014-06-05	2008-06-30		ENSG00000223756	ENSG00000223756			12384	pseudogene	pseudogene	"""tumor-supressing STF cDNA 2"", ""asparagine-linked glycosylation 1 homolog (yeast, beta-1,4-mannosyltransferase) (ALG1) pseudogene"""	608999	"""tumor suppressing subtransferable candidate 2"""			9403053	Standard	NR_024248		Approved				OTTHUMG00000011705		11.37:g.3427845C>T														0	962	+									RNA	SNP	ENST00000529482.1	37																																																																																						0.587	TSSC2-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000392020.1			8	212	0	0	0	1	0	8	212				
RPLP0P2	113157	broad.mit.edu	37	11	61405030	61405030	+	RNA	SNP	T	T	A			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr11:61405030T>A	ENST00000496593.1	+	0	1634					NR_002775.2				ribosomal protein, large, P0 pseudogene 2																		ctgctgctgctgcAGCCCCAG	0.552																																						ENST00000496593.1																			0																																																			0							g.chr11:61405030T>A	BC010523		11q12.2	2014-08-07			ENSG00000243742	ENSG00000243742		"""L ribosomal proteins"""	17960	pseudogene	pseudogene						19123937, 25089627	Standard	NR_002775		Approved		uc001nrz.1		OTTHUMG00000158396		11.37:g.61405030T>A								NR_002775.2						0	1634	+									RNA	SNP	ENST00000496593.1	37																																																																																						0.552	RPLP0P2-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000350911.1	NR_002775		6	225	0	0	0	1	0	6	225				
DNM1P47	100216544	broad.mit.edu	37	15	102304772	102304772	+	RNA	SNP	T	T	C	rs199967915	byFrequency	TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr15:102304772T>C	ENST00000561463.1	+	0	12818									DNM1 pseudogene 47																		CACAGCGGCGTGACGAGACTC	0.587																																						ENST00000561463.1																			0																																																			0							g.chr15:102304772T>C	AJ576276		15q26.3	2013-04-25			ENSG00000259660	ENSG00000259660			35200	pseudogene	pseudogene				DNM1DN14@			Standard	NG_009149		Approved	DNM1DN14-3			OTTHUMG00000172265		15.37:g.102304772T>C														0	12818	+									RNA	SNP	ENST00000561463.1	37																																																																																						0.587	DNM1P47-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000417589.1	NG_009149		8	42	0	0	0	1	0	8	42				
ERAP1	51752	broad.mit.edu	37	5	96122218	96122218	+	Missense_Mutation	SNP	C	C	T			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr5:96122218C>T	ENST00000443439.2	-	12	1781	c.1715G>A	c.(1714-1716)aGc>aAc	p.S572N	ERAP1_ENST00000514604.1_5'UTR|CTD-2260A17.1_ENST00000512856.1_RNA|ERAP1_ENST00000296754.3_Missense_Mutation_p.S572N|CTD-2260A17.1_ENST00000602972.1_RNA	NM_001040458.1|NM_001198541.1	NP_001035548.1|NP_001185470.1	Q9NZ08	ERAP1_HUMAN	endoplasmic reticulum aminopeptidase 1	572					angiogenesis (GO:0001525)|antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|fat cell differentiation (GO:0045444)|membrane protein ectodomain proteolysis (GO:0006509)|positive regulation of angiogenesis (GO:0045766)|regulation of blood pressure (GO:0008217)|regulation of innate immune response (GO:0045088)|response to bacterium (GO:0009617)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	aminopeptidase activity (GO:0004177)|interleukin-1, Type II receptor binding (GO:0005151)|interleukin-6 receptor binding (GO:0005138)|metalloexopeptidase activity (GO:0008235)|zinc ion binding (GO:0008270)			endometrium(7)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|stomach(2)	19		all_cancers(142;1.75e-06)|all_epithelial(76;3.08e-09)|all_lung(232;0.000435)|Lung NSC(167;0.000601)|Ovarian(225;0.024)|Colorectal(57;0.0432)|Breast(839;0.244)		all cancers(79;7.26e-15)|COAD - Colon adenocarcinoma(37;0.071)		GTCGGATTTGCTGGTGATGAA	0.348																																						ENST00000296754.3																			0				endometrium(7)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|stomach(2)	19						c.(1714-1716)aGc>aAc		endoplasmic reticulum aminopeptidase 1							117.0	113.0	114.0					5																	96122218		2203	4300	6503	SO:0001583	missense	51752				angiogenesis|antigen processing and presentation of endogenous peptide antigen via MHC class I|fat cell differentiation|membrane protein ectodomain proteolysis|regulation of blood pressure|regulation of innate immune response|response to bacterium	cytosol|endoplasmic reticulum lumen|endoplasmic reticulum membrane|extracellular region|integral to membrane	aminopeptidase activity|interleukin-1, Type II receptor binding|interleukin-6 receptor binding|metalloexopeptidase activity|zinc ion binding	g.chr5:96122218C>T	AB011097	CCDS4085.1, CCDS47250.1	5q15	2014-04-07			ENSG00000164307	ENSG00000164307			18173	protein-coding gene	gene with protein product	"""aminopeptidase regulator of TNFR1 shedding"", ""adipocyte-derived leucine aminopeptidase"", ""puromycin-insensitive leucyl-specific aminopeptidase"""	606832				10220586, 12189246, 16286653	Standard	NM_001198541		Approved	ARTS-1, A-LAP, PILS-AP, KIAA0525, ERAAP1	uc003kml.3	Q9NZ08	OTTHUMG00000128721	ENST00000443439.2:c.1715G>A	5.37:g.96122218C>T	ENSP00000406304:p.Ser572Asn					ERAP1_ENST00000443439.2_Missense_Mutation_p.S572N|ERAP1_ENST00000514604.1_5'UTR	p.S572N	NM_016442.3	NP_057526.3	Q9NZ08	ERAP1_HUMAN		all cancers(79;7.26e-15)|COAD - Colon adenocarcinoma(37;0.071)	12	1972	-		all_cancers(142;1.75e-06)|all_epithelial(76;3.08e-09)|all_lung(232;0.000435)|Lung NSC(167;0.000601)|Ovarian(225;0.024)|Colorectal(57;0.0432)|Breast(839;0.244)	572					O60278|Q6UWY6|Q8NEL4|Q8TAD0|Q9UHF8|Q9UKY2	Missense_Mutation	SNP	ENST00000443439.2	37	c.1715G>A	CCDS47250.1	.	.	.	.	.	.	.	.	.	.	C	14.70	2.612513	0.46631	.	.	ENSG00000164307	ENST00000296754;ENST00000443439;ENST00000414384	T;T	0.01369	4.97;4.97	5.33	5.33	0.75918	.	0.226724	0.51477	D	0.000090	T	0.03263	0.0095	L	0.58354	1.805	0.54753	D	0.999985	B;B;B	0.28400	0.013;0.028;0.21	B;B;B	0.33799	0.016;0.023;0.17	T	0.54262	-0.8320	10	0.40728	T	0.16	.	18.6209	0.91321	0.0:1.0:0.0:0.0	.	572;572;572	A8K6H1;Q9NZ08;Q9NZ08-2	.;ERAP1_HUMAN;.	N	572	ENSP00000296754:S572N;ENSP00000406304:S572N	ENSP00000296754:S572N	S	-	2	0	ERAP1	96147974	1.000000	0.71417	1.000000	0.80357	0.623000	0.37688	4.394000	0.59671	2.500000	0.84329	0.484000	0.47621	AGC		0.348	ERAP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370699.1	NM_016442		7	190	0	0	0	1	0	7	190				
RUNX2	860	broad.mit.edu	37	6	45390482	45390482	+	Missense_Mutation	SNP	C	C	G			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr6:45390482C>G	ENST00000371438.1	+	2	569	c.211C>G	c.(211-213)Cag>Gag	p.Q71E	RUNX2_ENST00000352853.5_Missense_Mutation_p.Q139E|RUNX2_ENST00000541979.1_Missense_Mutation_p.Q139E|RUNX2_ENST00000576263.1_Missense_Mutation_p.Q71E|RUNX2_ENST00000465038.2_Missense_Mutation_p.Q71E|RP1-244F24.1_ENST00000606796.1_RNA|RUNX2_ENST00000371436.6_Missense_Mutation_p.Q71E|RUNX2_ENST00000371432.3_Missense_Mutation_p.Q57E|RUNX2_ENST00000359524.5_Missense_Mutation_p.Q57E	NM_001024630.3	NP_001019801.3	Q13950	RUNX2_HUMAN	runt-related transcription factor 2	71	Poly-Gln.				BMP signaling pathway (GO:0030509)|cell maturation (GO:0048469)|cellular response to BMP stimulus (GO:0071773)|chondrocyte development (GO:0002063)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic forelimb morphogenesis (GO:0035115)|endochondral ossification (GO:0001958)|gene expression (GO:0010467)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis of dentin-containing tooth (GO:0042475)|ossification (GO:0001503)|osteoblast development (GO:0002076)|osteoblast differentiation (GO:0001649)|osteoblast fate commitment (GO:0002051)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus (GO:1901522)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|stem cell differentiation (GO:0048863)|T cell differentiation (GO:0030217)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(18)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34						gcagcagcagcaggaggcggc	0.716																																						ENST00000371438.1																			0				breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(18)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34						c.(211-213)Cag>Gag		runt-related transcription factor 2							6.0	10.0	9.0					6																	45390482		1279	2789	4068	SO:0001583	missense	860				negative regulation of transcription, DNA-dependent|osteoblast differentiation|positive regulation of transcription, DNA-dependent	nucleus	ATP binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity	g.chr6:45390482C>G	AF001450	CCDS43467.1, CCDS43468.1, CCDS43467.2, CCDS43468.2	6p21	2010-08-20			ENSG00000124813	ENSG00000124813			10472	protein-coding gene	gene with protein product		600211		CCD, CBFA1, CCD1		7835892	Standard	NM_001024630		Approved	AML3, PEBP2A1, PEBP2aA1	uc011dvx.2	Q13950	OTTHUMG00000014774	ENST00000371438.1:c.211C>G	6.37:g.45390482C>G	ENSP00000360493:p.Gln71Glu					RUNX2_ENST00000465038.2_Missense_Mutation_p.Q71E|RUNX2_ENST00000359524.5_Missense_Mutation_p.Q57E|RUNX2_ENST00000352853.5_Missense_Mutation_p.Q139E|RUNX2_ENST00000371432.3_Missense_Mutation_p.Q57E|RUNX2_ENST00000576263.1_Missense_Mutation_p.Q71E|RUNX2_ENST00000371436.6_Missense_Mutation_p.Q71E|RUNX2_ENST00000541979.1_Missense_Mutation_p.Q139E	p.Q71E	NM_001024630.3	NP_001019801.3	Q13950	RUNX2_HUMAN			2	569	+			71			Poly-Gln.		O14614|O14615|O95181	Missense_Mutation	SNP	ENST00000371438.1	37	c.211C>G	CCDS43467.2	.	.	.	.	.	.	.	.	.	.	C	12.60	1.985548	0.35036	.	.	ENSG00000124813	ENST00000465038;ENST00000352853;ENST00000541979;ENST00000371438;ENST00000371436;ENST00000359524;ENST00000371432	T;T;T;T;T;T;T	0.61742	0.08;0.08;0.08;0.08;0.08;0.08;0.08	3.45	3.45	0.39498	.	1.972660	0.03402	N	0.203449	T	0.19248	0.0462	N	0.14661	0.345	0.27094	N	0.962779	B;B;B	0.23806	0.033;0.055;0.091	B;B;B	0.20384	0.029;0.013;0.029	T	0.13818	-1.0495	10	0.02654	T	1	.	14.8379	0.70197	0.0:1.0:0.0:0.0	.	139;71;57	F6RGB9;Q13950;Q13950-2	.;RUNX2_HUMAN;.	E	71;139;139;71;71;57;57	ENSP00000420707:Q71E;ENSP00000319087:Q139E;ENSP00000446290:Q139E;ENSP00000360493:Q71E;ENSP00000360491:Q71E;ENSP00000352514:Q57E;ENSP00000360486:Q57E	ENSP00000319087:Q139E	Q	+	1	0	RUNX2	45498460	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	1.268000	0.33062	1.622000	0.50330	0.407000	0.27541	CAG		0.716	RUNX2-003	KNOWN	not_organism_supported|upstream_ATG|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040755.2	NM_004348		6	170	0	0	0	1	0	6	170				
LOC644669	644669	broad.mit.edu	37	18	15323347	15323347	+	RNA	SNP	T	T	C			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr18:15323347T>C	ENST00000455308.2	-	0	501				RNU6-721P_ENST00000410155.1_RNA	NR_027417.1																						CCAATAAAAGTGGTGTGTGGC	0.303																																						ENST00000455308.2																			0																																																			0							g.chr18:15323347T>C																													18.37:g.15323347T>C								NR_027417.1						0	501	-									RNA	SNP	ENST00000455308.2	37																																																																																						0.303	AP005901.1-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000373635.1			6	58	0	0	0	1	0	6	58				
EP400	57634	broad.mit.edu	37	12	132547087	132547087	+	Silent	SNP	G	G	A	rs12366766	byFrequency	TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr12:132547087G>A	ENST00000333577.4	+	48	8392	c.8283G>A	c.(8281-8283)caG>caA	p.Q2761Q	EP400_ENST00000332482.4_Silent_p.Q2688Q|EP400_ENST00000330386.6_Silent_p.Q2644Q|EP400_ENST00000389562.2_Silent_p.Q2724Q|EP400_ENST00000389561.2_Silent_p.Q2725Q			Q96L91	EP400_HUMAN	E1A binding protein p400	2761	Interaction with ZNF42. {ECO:0000250}.|Poly-Gln.				chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.Q2724Q(16)|p.Q2725Q(1)		NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		agcagcagcagcaacaacagc	0.562													G|||	37	0.00738818	0.0038	0.0072	5008	,	,		15585	0.002		0.0149	False		,,,				2504	0.0102					ENST00000333577.4																			17	Substitution - coding silent(17)	p.Q2724Q(16)|p.Q2725Q(1)	prostate(4)|kidney(4)|central_nervous_system(3)|lung(3)|endometrium(2)|urinary_tract(1)	NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161						c.(8281-8283)caG>caA		E1A binding protein p400							28.0	31.0	30.0					12																	132547087		2199	4282	6481	SO:0001819	synonymous_variant	57634				histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent	NuA4 histone acetyltransferase complex|nuclear speck	ATP binding|DNA binding|helicase activity	g.chr12:132547087G>A	U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"""trinucleotide repeat containing 12"""	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.8283G>A	12.37:g.132547087G>A						EP400_ENST00000330386.6_Silent_p.Q2644Q|EP400_ENST00000389562.2_Silent_p.Q2724Q|EP400_ENST00000389561.2_Silent_p.Q2725Q|EP400_ENST00000332482.4_Silent_p.Q2688Q	p.Q2761Q			Q96L91	EP400_HUMAN		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)	48	8392	+	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)	2761			Interaction with ZNF42 (By similarity).|Poly-Gln.		O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Silent	SNP	ENST00000333577.4	37	c.8283G>A																																																																																					0.562	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409		14	338	0	0	0	1	0	14	338				
LILRB5	10990	broad.mit.edu	37	19	54754843	54754843	+	Intron	SNP	A	A	G			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr19:54754843A>G	ENST00000316219.5	-	13	1734				LILRB5_ENST00000345866.6_Intron|CTD-2337J16.1_ENST00000595133.1_lincRNA|LILRB5_ENST00000449561.2_Intron|LILRB5_ENST00000450632.1_Missense_Mutation_p.S598P	NM_001081442.1|NM_006840.3	NP_001074911.1|NP_006831.1	O75023	LIRB5_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 5						cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)	integral component of membrane (GO:0016021)	transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	all_cancers(19;0.00681)|all_epithelial(19;0.00368)|all_lung(19;0.016)|Lung NSC(19;0.0296)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GGGGGTGGGGAGGCCTGGGGG	0.607																																						ENST00000450632.1																			0				NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	56						c.(1792-1794)Tcc>Ccc		leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 5							43.0	42.0	42.0					19																	54754843		2191	4270	6461	SO:0001627	intron_variant	0				cell surface receptor linked signaling pathway|defense response	integral to membrane	transmembrane receptor activity	g.chr19:54754843A>G	AF025534	CCDS12885.1, CCDS42611.1, CCDS46176.1	19q13.4	2013-01-11			ENSG00000105609	ENSG00000105609		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6609	protein-coding gene	gene with protein product		604814				9548455	Standard	NM_006840		Approved	LIR-8, LIR8, CD85c	uc002qey.3	O75023	OTTHUMG00000066636	ENST00000316219.5:c.1627-47T>C	19.37:g.54754843A>G						LILRB5_ENST00000449561.2_Intron|LILRB5_ENST00000345866.6_Intron|LILRB5_ENST00000316219.5_Intron	p.S598P			O75023	LIRB5_HUMAN		GBM - Glioblastoma multiforme(193;0.105)	13	1869	-	all_cancers(19;0.00681)|all_epithelial(19;0.00368)|all_lung(19;0.016)|Lung NSC(19;0.0296)|Ovarian(34;0.19)		423					Q8N760	Missense_Mutation	SNP	ENST00000316219.5	37	c.1792T>C	CCDS12885.1	.	.	.	.	.	.	.	.	.	.	A	10.02	1.237390	0.22711	.	.	ENSG00000105609	ENST00000450632	T	0.00497	6.98	1.74	-0.656	0.11436	.	.	.	.	.	T	0.00328	0.0010	.	.	.	0.09310	N	1	B	0.24576	0.106	B	0.17433	0.018	T	0.45702	-0.9243	8	0.87932	D	0	.	1.6956	0.02861	0.475:0.0:0.2022:0.3228	.	598	C9JMK7	.	P	598	ENSP00000414225:S598P	ENSP00000414225:S598P	S	-	1	0	LILRB5	59446655	0.000000	0.05858	0.043000	0.18650	0.608000	0.37181	-0.873000	0.04214	-0.256000	0.09473	0.332000	0.21555	TCC		0.607	LILRB5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142877.2			10	248	0	0	0	1	0	10	248				
NBPF1	55672	broad.mit.edu	37	1	16918653	16918653	+	Splice_Site	SNP	C	C	T			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr1:16918653C>T	ENST00000430580.2	-	6	853		c.e6+1			NM_017940.3	NP_060410.2	Q3BBV0	NBPF1_HUMAN	neuroblastoma breakpoint family, member 1							cytoplasm (GO:0005737)									UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		TCTTAACTTACTGTTGTGAAA	0.418																																						ENST00000430580.2																			0											c.e6+1		neuroblastoma breakpoint family, member 1																																				SO:0001630	splice_region_variant	55672					cytoplasm		g.chr1:16918653C>T	AB051480		1p36.13	2013-01-30			ENSG00000219481	ENSG00000219481		"""neuroblastoma breakpoint family"""	26088	protein-coding gene	gene with protein product		610501				11214970, 16079250	Standard	NM_017940		Approved	FLJ20719, KIAA1693	uc001ayw.4	Q3BBV0	OTTHUMG00000002487	ENST00000430580.2:c.34+1G>A	1.37:g.16918653C>T								NM_017940.3	NP_060410.2	Q3BBV0	NBPF1_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)	6	853	-								Q8N4E8|Q9C0H0	Splice_Site	SNP	ENST00000430580.2	37																																																																																						0.418	NBPF1-005	NOVEL	upstream_uORF|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000106436.3	NM_017940	Intron	21	385	0	0	0	1	0	21	385				
CCT6P1	643253	broad.mit.edu	37	7	65222986	65222986	+	RNA	SNP	G	G	T			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr7:65222986G>T	ENST00000442266.1	+	0	578				SNORA15_ENST00000384058.1_RNA|SNORA22_ENST00000383907.1_RNA					chaperonin containing TCP1, subunit 6 (zeta) pseudogene 1																		GAATTCTGGCGTTTTTTACAA	0.289																																						ENST00000442266.1																			0																																																			0							g.chr7:65222986G>T	BC052238, BC073761		7q11.21	2010-06-29	2008-09-22	2008-09-22	ENSG00000228409	ENSG00000228409			33094	pseudogene	pseudogene			"""chaperonin containing TCP1, subunit 6A (zeta 1) pseudogene 1"""	CCT6AP1			Standard	NR_003110		Approved		uc003tug.3		OTTHUMG00000156733		7.37:g.65222986G>T														0	578	+									RNA	SNP	ENST00000442266.1	37																																																																																						0.289	CCT6P1-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000345507.1	NR_003110		7	82	1	0	0.00307968	1	0.00307968	7	82				
MLLT3	4300	broad.mit.edu	37	9	20414343	20414343	+	Silent	SNP	A	A	G	rs372894655	byFrequency	TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr9:20414343A>G	ENST00000380338.4	-	5	787	c.501T>C	c.(499-501)agT>agC	p.S167S	MLLT3_ENST00000429426.2_Silent_p.S164S|MLLT3_ENST00000475957.1_5'UTR|MLLT3_ENST00000355930.6_5'UTR	NM_004529.2	NP_004520.2	P42568	AF9_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3	167	Poly-Ser.				anterior/posterior pattern specification (GO:0009952)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|regulation of transcription, DNA-templated (GO:0006355)|segment specification (GO:0007379)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)		p.S167S(19)		central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(6)|lung(24)|ovary(1)|prostate(4)|skin(1)|urinary_tract(7)	66				GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)		tgctgctgctactgctgctgc	0.532			T	MLL	ALL								A|||	612	0.122204	0.1505	0.1066	5008	,	,		12422	0.0833		0.0716	False		,,,				2504	0.1871					ENST00000380338.4				Dom	yes		9	9p22	4300	T	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3 (AF9)"""			L	MLL		ALL		19	Substitution - coding silent(19)	p.S167S(19)	lung(8)|kidney(5)|endometrium(3)|central_nervous_system(1)|urinary_tract(1)|prostate(1)	central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(6)|lung(24)|ovary(1)|prostate(4)|skin(1)|urinary_tract(7)	66						c.(499-501)agT>agC		myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3							8.0	15.0	13.0					9																	20414343		1537	3257	4794	SO:0001819	synonymous_variant	4300				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding	g.chr9:20414343A>G	L13744	CCDS6494.1	9p22	2008-02-05	2001-11-28		ENSG00000171843	ENSG00000171843			7136	protein-coding gene	gene with protein product		159558	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 3"""			8506309, 8414510	Standard	NM_001286691		Approved	AF-9, AF9, YEATS3	uc003zoe.2	P42568	OTTHUMG00000019650	ENST00000380338.4:c.501T>C	9.37:g.20414343A>G						MLLT3_ENST00000475957.1_5'UTR|MLLT3_ENST00000355930.6_5'UTR|MLLT3_ENST00000429426.2_Silent_p.S164S	p.S167S	NM_004529.2	NP_004520.2	P42568	AF9_HUMAN		GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)	5	787	-			167			Poly-Ser.		B1AMQ2|B2R7B3|B7Z755|D3DRJ8|Q8IVB0	Silent	SNP	ENST00000380338.4	37	c.501T>C	CCDS6494.1																																																																																				0.532	MLLT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051872.1	NM_004529		39	462	0	0	0	1	0	39	462				
WASH3P	374666	broad.mit.edu	37	15	102515335	102515335	+	RNA	SNP	C	C	G	rs201001946		TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr15:102515335C>G	ENST00000557932.1	+	0	1181				DDX11L9_ENST00000562189.1_RNA			C4AMC7	WASH3_HUMAN	WAS protein family homolog 3 pseudogene						Arp2/3 complex-mediated actin nucleation (GO:0034314)|endosomal transport (GO:0016197)|retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|membrane (GO:0016020)|recycling endosome (GO:0055037)|WASH complex (GO:0071203)	alpha-tubulin binding (GO:0043014)	p.L386V(3)		central_nervous_system(1)|endometrium(6)|kidney(11)|prostate(5)|stomach(1)|urinary_tract(1)	25						GGAGCGAAAGCTGGAGAAGAA	0.652																																						ENST00000557932.1																			3	Substitution - Missense(3)	p.L386V(3)	prostate(2)|kidney(1)	central_nervous_system(1)|endometrium(6)|kidney(11)|prostate(5)|stomach(1)|urinary_tract(1)	25																																														0							g.chr15:102515335C>G			15q26.3	2014-03-20	2008-01-16	2008-01-16	ENSG00000185596	ENSG00000185596		"""WAS protein homologs"""	24362	pseudogene	pseudogene			"""family with sequence similarity 39, member D pseudogene"""	FAM39DP		11701968, 18159949	Standard	NR_003659		Approved	FLJ25222	uc002cdi.3	C4AMC7	OTTHUMG00000172275		15.37:g.102515335C>G														0	1181	+									RNA	SNP	ENST00000557932.1	37			.	.	.	.	.	.	.	.	.	.	c	1.538	-0.542507	0.04053	.	.	ENSG00000185596	ENST00000338304;ENST00000398121	.	.	.	1.01	1.01	0.19927	.	0.125321	0.53938	D	0.000056	T	0.41926	0.1180	.	.	.	.	.	.	.	.	.	.	.	.	T	0.51044	-0.8755	4	.	.	.	-11.5249	7.9382	0.29941	0.0:1.0:0.0:0.0	.	.	.	.	V	395;386	.	.	L	+	1	2	WASH3P	100332858	1.000000	0.71417	0.999000	0.59377	0.392000	0.30506	1.146000	0.31589	0.863000	0.35553	0.184000	0.17185	CTG		0.652	WASH3P-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000417608.1	NM_199163		9	92	0	0	0	1	0	9	92				
OR2M5	127059	broad.mit.edu	37	1	248309032	248309032	+	Missense_Mutation	SNP	T	T	G			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr1:248309032T>G	ENST00000366476.1	+	1	583	c.583T>G	c.(583-585)Ttt>Gtt	p.F195V		NM_001004690.1	NP_001004690.1	A3KFT3	OR2M5_HUMAN	olfactory receptor, family 2, subfamily M, member 5	195						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(5)|kidney(2)|large_intestine(7)|liver(1)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	49	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0388)			CACATCAATATTTGAAAAGGT	0.413																																						ENST00000366476.1																			0				NS(1)|endometrium(5)|kidney(2)|large_intestine(7)|liver(1)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	49						c.(583-585)Ttt>Gtt		olfactory receptor, family 2, subfamily M, member 5							265.0	260.0	262.0					1																	248309032		2203	4300	6503	SO:0001583	missense	127059				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr1:248309032T>G		CCDS31105.1	1q44	2012-08-09		2004-03-10	ENSG00000162727	ENSG00000162727		"""GPCR / Class A : Olfactory receptors"""	19576	protein-coding gene	gene with protein product				OR2M5P			Standard	NM_001004690		Approved		uc010pze.2	A3KFT3	OTTHUMG00000040447	ENST00000366476.1:c.583T>G	1.37:g.248309032T>G	ENSP00000355432:p.Phe195Val						p.F195V	NM_001004690.1	NP_001004690.1	A3KFT3	OR2M5_HUMAN	OV - Ovarian serous cystadenocarcinoma(106;0.0388)		1	583	+	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		195						Missense_Mutation	SNP	ENST00000366476.1	37	c.583T>G	CCDS31105.1	.	.	.	.	.	.	.	.	.	.	t	17.11	3.306046	0.60305	.	.	ENSG00000162727	ENST00000366476	T	0.00058	8.79	3.52	-0.472	0.12115	GPCR, rhodopsin-like superfamily (1);	0.000000	0.32935	U	0.005464	T	0.00178	0.0005	L	0.27944	0.81	0.09310	N	1	P	0.50369	0.934	P	0.59643	0.861	T	0.51348	-0.8717	10	0.87932	D	0	.	3.1108	0.06357	0.3969:0.2566:0.0:0.3465	.	195	A3KFT3	OR2M5_HUMAN	V	195	ENSP00000355432:F195V	ENSP00000355432:F195V	F	+	1	0	OR2M5	246375655	0.173000	0.23056	0.041000	0.18516	0.397000	0.30659	0.092000	0.15066	0.359000	0.24239	0.403000	0.27427	TTT		0.413	OR2M5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097343.1	NM_001004690		26	1667	0	0	0	1	0	26	1667				
KMT2C	58508	broad.mit.edu	37	7	151935851	151935851	+	Missense_Mutation	SNP	C	C	A			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr7:151935851C>A	ENST00000262189.6	-	15	2811	c.2593G>T	c.(2593-2595)Ggt>Tgt	p.G865C	KMT2C_ENST00000355193.2_Missense_Mutation_p.G865C	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	865					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										ATTTCCCGACCTTCTGAAATG	0.423																																						ENST00000355193.2																			0											c.(2593-2595)Ggt>Tgt		lysine (K)-specific methyltransferase 2C							49.0	52.0	51.0					7																	151935851		2201	4300	6501	SO:0001583	missense	58508							g.chr7:151935851C>A	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	13726	protein-coding gene	gene with protein product		606833	"""myeloid/lymphoid or mixed-lineage leukemia 3"""	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.2593G>T	7.37:g.151935851C>A	ENSP00000262189:p.Gly865Cys					KMT2C_ENST00000262189.6_Missense_Mutation_p.G865C	p.G865C							15	2811	-								Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	c.2593G>T	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	C	19.14	3.770503	0.69992	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	D;D	0.86030	-2.06;-2.06	5.53	5.53	0.82687	.	0.000000	0.45126	D	0.000398	D	0.91395	0.7285	L	0.56769	1.78	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	D	0.91517	0.5231	10	0.72032	D	0.01	.	19.8258	0.96617	0.0:1.0:0.0:0.0	.	865	Q8NEZ4	MLL3_HUMAN	C	865	ENSP00000262189:G865C;ENSP00000347325:G865C	ENSP00000262189:G865C	G	-	1	0	MLL3	151566784	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.442000	0.80503	2.749000	0.94314	0.650000	0.86243	GGT		0.423	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			15	594	1	0	6.49762e-13	1	7.3576e-13	15	594				
DGCR14	8220	broad.mit.edu	37	22	19132062	19132062	+	Missense_Mutation	SNP	G	G	A	rs113904207	byFrequency	TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr22:19132062G>A	ENST00000252137.6	-	1	135	c.92C>T	c.(91-93)gCg>gTg	p.A31V		NM_022719.2	NP_073210.1	Q96DF8	DGC14_HUMAN	DiGeorge syndrome critical region gene 14	31			A -> V (in dbSNP:rs113904207). {ECO:0000269|PubMed:9063747}.		mRNA splicing, via spliceosome (GO:0000398)|nervous system development (GO:0007399)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)	16	Colorectal(54;0.0993)					CTTGCTCGTCGCAGCCCCAGC	0.677													G|||	20	0.00399361	0.0008	0.0043	5008	,	,		13281	0.0		0.0089	False		,,,				2504	0.0072					ENST00000252137.6																			0				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)	16						c.(91-93)gCg>gTg		DiGeorge syndrome critical region gene 14		G	VAL/ALA	8,4390		0,8,2191	21.0	20.0	20.0		92	-2.3	0.0	22	dbSNP_132	20	134,8454		4,126,4164	no	missense	DGCR14	NM_022719.2	64	4,134,6355	AA,AG,GG		1.5603,0.1819,1.0935	benign	31/477	19132062	142,12844	2199	4294	6493	SO:0001583	missense	8220				nervous system development	catalytic step 2 spliceosome		g.chr22:19132062G>A	L77566	CCDS13756.1	22q11.21	2007-02-20			ENSG00000100056	ENSG00000100056			16817	protein-coding gene	gene with protein product		601755	"""DiGeorge syndrome critical region gene 13"""	DGCR13		8776594, 9063747	Standard	NM_022719		Approved	DGSI, Es2el, ES2, DGS-H	uc002zou.3	Q96DF8	OTTHUMG00000150119	ENST00000252137.6:c.92C>T	22.37:g.19132062G>A	ENSP00000252137:p.Ala31Val						p.A31V	NM_022719.2	NP_073210.1	Q96DF8	DGC14_HUMAN			1	135	-	Colorectal(54;0.0993)		31		A -> V.			Q49AH7|Q9BTZ4	Missense_Mutation	SNP	ENST00000252137.6	37	c.92C>T	CCDS13756.1	10	0.004578754578754579	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	8	0.010554089709762533	G	17.58	3.423987	0.62733	0.001819	0.015603	ENSG00000100056	ENST00000252137	T	0.23754	1.89	3.61	-2.28	0.06826	.	0.753410	0.12075	N	0.501882	T	0.04137	0.0115	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.35599	-0.9782	10	0.13108	T	0.6	-2.8334	5.0031	0.14275	0.3495:0.1435:0.507:0.0	.	31	Q96DF8	DGC14_HUMAN	V	31	ENSP00000252137:A31V	ENSP00000252137:A31V	A	-	2	0	DGCR14	17512062	0.001000	0.12720	0.012000	0.15200	0.728000	0.41692	1.058000	0.30504	-0.315000	0.08703	-0.499000	0.04595	GCG		0.677	DGCR14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316432.2			6	146	0	0	0	1	0	6	146				
TUBB8P7	197331	broad.mit.edu	37	16	90161902	90161902	+	RNA	SNP	A	A	G	rs6500471	byFrequency	TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr16:90161902A>G	ENST00000564451.1	+	0	1255				TUBB8P7_ENST00000567960.1_RNA					tubulin, beta 8 class VIII pseudogene 7									p.K213R(8)									ATATGTTCCAAGACCCTAAAA	0.537													.|||	3135	0.625998	0.9327	0.5014	5008	,	,		11498	0.7867		0.4702	False		,,,				2504	0.2945					ENST00000564451.1																			8	Substitution - Missense(8)	p.K213R(8)	kidney(4)|prostate(3)|urinary_tract(1)																																																0							g.chr16:90161902A>G			16q24.3	2013-02-18			ENSG00000261812	ENSG00000261812			42345	pseudogene	pseudogene							Standard	NG_002334		Approved				OTTHUMG00000172847		16.37:g.90161902A>G						TUBB8P7_ENST00000567960.1_RNA								0	1255	+									RNA	SNP	ENST00000564451.1	37																																																																																						0.537	TUBB8P7-004	KNOWN	basic	processed_transcript	polymorphic_pseudogene	OTTHUMT00000420856.1	NG_002334		12	213	0	0	0	1	0	12	213				
NUAK1	9891	broad.mit.edu	37	12	106532400	106532400	+	Missense_Mutation	SNP	T	T	C	rs201298691		TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr12:106532400T>C	ENST00000261402.2	-	1	1411	c.32A>G	c.(31-33)gAc>gGc	p.D11G		NM_014840.2	NP_055655.1	O60285	NUAK1_HUMAN	NUAK family, SNF1-like kinase, 1	11					cell adhesion (GO:0007155)|cellular response to DNA damage stimulus (GO:0006974)|regulation of cell adhesion (GO:0030155)|regulation of cell proliferation (GO:0042127)|regulation of cellular senescence (GO:2000772)|regulation of myosin-light-chain-phosphatase activity (GO:0035507)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(13)|ovary(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	37						GTCGGGGCGGTCCCCCGCCAC	0.771																																						ENST00000261402.2																			0				NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(13)|ovary(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	37						c.(31-33)gAc>gGc		NUAK family, SNF1-like kinase, 1							4.0	5.0	5.0					12																	106532400		2004	3866	5870	SO:0001583	missense	9891						ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity	g.chr12:106532400T>C	AB011109	CCDS31892.1	12q23.3	2005-08-09				ENSG00000074590			14311	protein-coding gene	gene with protein product	"""AMP-activated protein kinase family member 5"""	608130				12409306, 13679856	Standard	NM_014840		Approved	ARK5, KIAA0537, NuaK1	uc001tlj.1	O60285	OTTHUMG00000169763	ENST00000261402.2:c.32A>G	12.37:g.106532400T>C	ENSP00000261402:p.Asp11Gly						p.D11G	NM_014840.2	NP_055655.1	O60285	NUAK1_HUMAN			1	1411	-			11					A7MD39|Q96KA8	Missense_Mutation	SNP	ENST00000261402.2	37	c.32A>G	CCDS31892.1	.	.	.	.	.	.	.	.	.	.	T	5.712	0.315837	0.10789	.	.	ENSG00000074590	ENST00000261402;ENST00000359413	T	0.72942	-0.7	2.76	1.52	0.23074	.	0.497641	0.16531	U	0.210347	T	0.44456	0.1294	N	0.08118	0	0.09310	N	1	B	0.15930	0.015	B	0.08055	0.003	T	0.31024	-0.9958	10	0.49607	T	0.09	.	4.6048	0.12372	0.0:0.1699:0.0:0.8301	.	11	O60285	NUAK1_HUMAN	G	11	ENSP00000261402:D11G	ENSP00000261402:D11G	D	-	2	0	NUAK1	105056530	0.000000	0.05858	0.774000	0.31636	0.236000	0.25371	-0.289000	0.08365	1.154000	0.42482	0.260000	0.18958	GAC		0.771	NUAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405767.2	NM_014840		12	29	0	0	0	1	0	12	29				
LOC644669	644669	broad.mit.edu	37	18	15323276	15323276	+	RNA	SNP	A	A	T	rs200953619		TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr18:15323276A>T	ENST00000455308.2	-	0	572				RNU6-721P_ENST00000410155.1_RNA	NR_027417.1																						ATCAACTGCAATTGCATTTGC	0.308																																						ENST00000455308.2																			0																																																			0							g.chr18:15323276A>T																													18.37:g.15323276A>T								NR_027417.1						0	572	-									RNA	SNP	ENST00000455308.2	37																																																																																						0.308	AP005901.1-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000373635.1			26	72	0	0	0	1	0	26	72				
OR2T2	401992	broad.mit.edu	37	1	248616734	248616734	+	Silent	SNP	A	A	G	rs201716034|rs376194718		TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr1:248616734A>G	ENST00000342927.3	+	1	658	c.636A>G	c.(634-636)ctA>ctG	p.L212L		NM_001004136.1	NP_001004136.1	Q6IF00	OR2T2_HUMAN	olfactory receptor, family 2, subfamily T, member 2	212						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(21)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	37	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TTATCCCTCTATCTGTCATCT	0.542																																						ENST00000342927.3																			0				cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(21)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	37						c.(634-636)ctA>ctG		olfactory receptor, family 2, subfamily T, member 2		A		0,4380		0,0,2190	210.0	143.0	166.0		636	-2.2	0.0	1		166	1,8523	1.2+/-3.3	0,1,4261	no	coding-synonymous	OR2T2	NM_001004136.1		0,1,6451	GG,GA,AA		0.0117,0.0,0.0077		212/325	248616734	1,12903	2190	4262	6452	SO:0001819	synonymous_variant	401992				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr1:248616734A>G	BK004462	CCDS31116.1	1q44	2012-08-09	2002-11-13	2002-11-15	ENSG00000196240	ENSG00000196240		"""GPCR / Class A : Olfactory receptors"""	14725	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily T, member 2 pseudogene"""	OR2T2P		14983052	Standard	NM_001004136		Approved		uc001iek.1	Q6IF00	OTTHUMG00000040480	ENST00000342927.3:c.636A>G	1.37:g.248616734A>G							p.L212L	NM_001004136.1	NP_001004136.1	Q6IF00	OR2T2_HUMAN	OV - Ovarian serous cystadenocarcinoma(106;0.0265)		1	658	+	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		212					B2RNM1|B9EH01	Silent	SNP	ENST00000342927.3	37	c.636A>G	CCDS31116.1																																																																																				0.542	OR2T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097421.1	NM_001004136		11	263	0	0	0	1	0	11	263				
HSD17B7P2	158160	broad.mit.edu	37	10	38654432	38654432	+	RNA	SNP	A	A	G	rs2257765		TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr10:38654432A>G	ENST00000494540.1	+	0	599					NR_003086.1				hydroxysteroid (17-beta) dehydrogenase 7 pseudogene 2																		TCATCTCGCAATGCAAGGAAA	0.453																																						ENST00000494540.1																			0																																																			0							g.chr10:38654432A>G			10p11.1	2011-06-29			ENSG00000099251	ENSG00000099251			28120	pseudogene	pseudogene						10544267	Standard	NR_003086		Approved	HSD17B7, bA291L22.1	uc010qex.1		OTTHUMG00000017993		10.37:g.38654432A>G								NR_003086.1						0	599	+									RNA	SNP	ENST00000494540.1	37																																																																																						0.453	HSD17B7P2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000047631.2	NR_003086		8	275	0	0	0	1	0	8	275				
LRRC37A4P	55073	broad.mit.edu	37	17	43587730	43587730	+	RNA	SNP	A	A	C			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr17:43587730A>C	ENST00000579913.1	-	0	1394				RP11-798G7.5_ENST00000253803.2_RNA	NR_002940.2				leucine rich repeat containing 37, member A4, pseudogene																		GTATTGATTCATTTTATTCAT	0.343																																						ENST00000253803.2																			0																																																			0							g.chr17:43587730A>C	AK000982		17q21.31	2014-04-01	2012-03-07	2012-03-07	ENSG00000214425	ENSG00000214425			25479	pseudogene	pseudogene			"""leucine rich repeat containing 37, member A4 (pseudogene)"""	LRRC37A4			Standard	NR_002940		Approved	FLJ10120	uc031rhd.1		OTTHUMG00000179212		17.37:g.43587730A>C						LRRC37A4P_ENST00000579913.1_RNA								0	267	+									RNA	SNP	ENST00000579913.1	37																																																																																						0.343	LRRC37A4P-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000445300.1	NR_002940		10	160	0	0	0	1	0	10	160				
LOC644669	644669	broad.mit.edu	37	18	15323336	15323336	+	RNA	SNP	G	G	A	rs199831831		TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr18:15323336G>A	ENST00000455308.2	-	0	512				RNU6-721P_ENST00000410155.1_RNA	NR_027417.1																						TTTCCTTATGGCCAATAAAAG	0.289													G|||	1	0.000199681	0.0	0.0	5008	,	,		16958	0.0		0.001	False		,,,				2504	0.0					ENST00000455308.2																			0																																																			0							g.chr18:15323336G>A																													18.37:g.15323336G>A								NR_027417.1						0	512	-									RNA	SNP	ENST00000455308.2	37																																																																																						0.289	AP005901.1-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000373635.1			5	55	0	0	0	1	0	5	55				
CHEK2	11200	broad.mit.edu	37	22	29091840	29091840	+	Missense_Mutation	SNP	T	T	C	rs142470496	byFrequency	TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr22:29091840T>C	ENST00000405598.1	-	12	1308	c.1117A>G	c.(1117-1119)Aag>Gag	p.K373E	CHEK2_ENST00000464581.1_5'Flank|CHEK2_ENST00000382580.2_Missense_Mutation_p.K416E|CHEK2_ENST00000544772.1_Missense_Mutation_p.K152E|CHEK2_ENST00000382566.1_3'UTR|CHEK2_ENST00000382578.1_Missense_Mutation_p.K282E|CHEK2_ENST00000328354.6_Missense_Mutation_p.K373E|CHEK2_ENST00000382565.1_Intron|CHEK2_ENST00000402731.1_Missense_Mutation_p.K344E|CHEK2_ENST00000404276.1_Missense_Mutation_p.K373E|CHEK2_ENST00000403642.1_Missense_Mutation_p.K282E|CHEK2_ENST00000348295.3_Missense_Mutation_p.K344E			O96017	CHK2_HUMAN	checkpoint kinase 2	373	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.|T-loop/activation segment.				cellular protein catabolic process (GO:0044257)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|double-strand break repair (GO:0006302)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|replicative senescence (GO:0090399)|response to gamma radiation (GO:0010332)|signal transduction in response to DNA damage (GO:0042770)|signal transduction involved in intra-S DNA damage checkpoint (GO:0072428)|spindle assembly involved in mitosis (GO:0090307)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|PML body (GO:0016605)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)	p.K373E(9)		central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						CCCAAAATCTTGGAGTGCCCA	0.418			F			breast		Direct reversal of damage;Other conserved DNA damage response genes																														ENST00000544772.1			yes	Rec		familial breast cancer	22	22q12.1	11200	F	CHK2 checkpoint homolog (S. pombe)			E		breast			9	Substitution - Missense(9)	p.K373E(9)	kidney(4)|prostate(2)|endometrium(1)|stomach(1)|central_nervous_system(1)	central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						c.(454-456)Aag>Gag	Direct reversal of damage;Other conserved DNA damage response genes	checkpoint kinase 2																																				SO:0001583	missense	11200				cell cycle|DNA damage checkpoint|DNA damage response, signal transduction resulting in induction of apoptosis|replicative senescence	PML body	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity	g.chr22:29091840T>C	AF086904	CCDS13843.1, CCDS13844.1, CCDS33629.1	22q12.1	2014-09-17	2011-11-11	2001-09-27	ENSG00000183765	ENSG00000183765			16627	protein-coding gene	gene with protein product		604373	"""CHK2 (checkpoint, S.pombe) homolog"", ""CHK2 checkpoint homolog (S. pombe)"""	RAD53		9836640, 10097108	Standard	NM_001257387		Approved	CDS1, CHK2, HuCds1, PP1425, bA444G7	uc003adt.1	O96017	OTTHUMG00000151023	ENST00000405598.1:c.1117A>G	22.37:g.29091840T>C	ENSP00000386087:p.Lys373Glu					CHEK2_ENST00000382566.1_3'UTR|CHEK2_ENST00000402731.1_Missense_Mutation_p.K344E|CHEK2_ENST00000348295.3_Missense_Mutation_p.K344E|CHEK2_ENST00000382580.2_Missense_Mutation_p.K416E|CHEK2_ENST00000328354.6_Missense_Mutation_p.K373E|CHEK2_ENST00000382565.1_Intron|CHEK2_ENST00000404276.1_Missense_Mutation_p.K373E|CHEK2_ENST00000405598.1_Missense_Mutation_p.K373E|CHEK2_ENST00000382578.1_Missense_Mutation_p.K282E|CHEK2_ENST00000403642.1_Missense_Mutation_p.K282E	p.K152E	NM_001257387.1	NP_001244316.1	O96017	CHK2_HUMAN			12	1890	-			373			FHA.		A8K3Y9|B7ZBF3|B7ZBF4|B7ZBF5|Q6QA03|Q6QA04|Q6QA05|Q6QA06|Q6QA07|Q6QA08|Q6QA10|Q6QA11|Q6QA12|Q6QA13|Q9HBS5|Q9HCQ8|Q9UGF0|Q9UGF1	Missense_Mutation	SNP	ENST00000405598.1	37	c.454A>G	CCDS13843.1	.	.	.	.	.	.	.	.	.	.	T	19.06	3.754336	0.69648	.	.	ENSG00000183765	ENST00000348295;ENST00000382578;ENST00000544772;ENST00000328354;ENST00000404276;ENST00000405598;ENST00000382580;ENST00000403642;ENST00000402731	T;T;T;T;T;T;T;T;T	0.54071	0.9;0.59;0.59;0.59;0.59;0.59;0.59;0.59;0.9	5.89	5.89	0.94794	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.043710	0.85682	D	0.000000	T	0.56292	0.1975	N	0.11756	0.17	0.80722	D	1	D;D;D;D;D;D	0.76494	0.996;0.999;0.998;0.998;0.993;0.991	P;D;D;D;D;P	0.74674	0.905;0.984;0.943;0.969;0.923;0.896	T	0.64769	-0.6329	10	0.87932	D	0	-1.7726	15.4726	0.75453	0.0:0.0:0.0:1.0	.	282;152;373;344;373;416	O96017-4;Q9HBS5;A8JZZ5;O96017-12;O96017;O96017-9	.;.;.;.;CHK2_HUMAN;.	E	344;282;152;373;373;373;416;282;344	ENSP00000329012:K344E;ENSP00000372021:K282E;ENSP00000442458:K152E;ENSP00000329178:K373E;ENSP00000385747:K373E;ENSP00000386087:K373E;ENSP00000372023:K416E;ENSP00000384919:K282E;ENSP00000384835:K344E	ENSP00000329178:K373E	K	-	1	0	CHEK2	27421840	1.000000	0.71417	1.000000	0.80357	0.479000	0.33129	4.270000	0.58896	2.248000	0.74166	0.528000	0.53228	AAG		0.418	CHEK2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321150.1	NM_001005735		10	315	0	0	0	1	0	10	315				
ANKRD20A8P	729171	broad.mit.edu	37	2	95522772	95522772	+	RNA	SNP	T	T	C	rs368571207		TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr2:95522772T>C	ENST00000432432.2	-	0	255					NR_040113.1		Q5CZ79	AN20B_HUMAN	ankyrin repeat domain 20 family, member A8, pseudogene									p.E49G(1)									GCGCTCCACCTCCGCGGCGTC	0.682																																						ENST00000432432.2																			1	Substitution - Missense(1)	p.E49G(1)	kidney(1)																																																0							g.chr2:95522772T>C			2q11.1	2011-09-16	2010-12-15	2010-12-15	ENSG00000229089	ENSG00000229089			23666	pseudogene	pseudogene			"""ankyrin repeat domain 20B"""	ANKRD20B			Standard	NR_003366		Approved		uc010fhq.2	Q5CZ79	OTTHUMG00000155138		2.37:g.95522772T>C								NR_040113.1						0	255	-								A6NC18	RNA	SNP	ENST00000432432.2	37																																																																																						0.682	ANKRD20A8P-002	KNOWN	not_best_in_genome_evidence|basic	processed_transcript	pseudogene	OTTHUMT00000451404.1			10	309	0	0	0	1	0	10	309				
LAPTM4B	55353	broad.mit.edu	37	8	98788187	98788187	+	Missense_Mutation	SNP	T	T	G			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr8:98788187T>G	ENST00000445593.2	+	1	903	c.223T>G	c.(223-225)Tcg>Gcg	p.S75A	LAPTM4B_ENST00000521545.2_5'UTR|RNU7-177P_ENST00000517101.1_RNA	NM_018407.4	NP_060877.3	Q86VI4	LAP4B_HUMAN	lysosomal protein transmembrane 4 beta	128					transport (GO:0006810)	integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(2)|skin(1)|stomach(1)	10	Breast(36;1.59e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.149)			GGCGAGGCGGTCGACGCTCCT	0.741																																						ENST00000445593.2																			0				breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(2)|skin(1)|stomach(1)	10						c.(223-225)Tcg>Gcg		lysosomal protein transmembrane 4 beta							4.0	5.0	5.0					8																	98788187		1948	3880	5828	SO:0001583	missense	55353				transport	endomembrane system|integral to membrane	protein binding	g.chr8:98788187T>G	AF317417	CCDS6275.1	8q22.1	2008-08-11	2008-08-11		ENSG00000104341	ENSG00000104341			13646	protein-coding gene	gene with protein product		613296					Standard	NM_018407		Approved	LC27	uc003yia.3	Q86VI4	OTTHUMG00000164740	ENST00000445593.2:c.223T>G	8.37:g.98788187T>G	ENSP00000402301:p.Ser75Ala					LAPTM4B_ENST00000521545.2_5'UTR	p.S75A	NM_018407.4	NP_060877.3	Q86VI4	LAP4B_HUMAN	OV - Ovarian serous cystadenocarcinoma(57;0.149)		1	903	+	Breast(36;1.59e-06)		128					Q3ZCV5|Q7L909|Q86VH8|Q9H060	Missense_Mutation	SNP	ENST00000445593.2	37	c.223T>G	CCDS6275.1	.	.	.	.	.	.	.	.	.	.	T	10.71	1.427158	0.25726	.	.	ENSG00000104341	ENST00000445593;ENST00000378722	T	0.45668	0.89	4.29	-6.6	0.01824	.	3.498930	0.01489	N	0.017004	T	0.17831	0.0428	N	0.08118	0	0.09310	N	0.999995	B;B	0.10296	0.003;0.0	B;B	0.10450	0.005;0.001	T	0.09207	-1.0685	10	0.18276	T	0.48	-0.39	2.7135	0.05181	0.1155:0.3244:0.3933:0.1668	.	75;128	Q86SJ0;Q86VI4	.;LAP4B_HUMAN	A	75;121	ENSP00000402301:S75A	ENSP00000367995:S121A	S	+	1	0	LAPTM4B	98857363	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.241000	0.01196	-1.056000	0.03205	-0.329000	0.08387	TCG		0.741	LAPTM4B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000380014.1			5	38	0	0	0	1	0	5	38				
LPIN2	9663	broad.mit.edu	37	18	2922157	2922157	+	Missense_Mutation	SNP	C	C	T			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr18:2922157C>T	ENST00000261596.4	-	17	2453	c.2215G>A	c.(2215-2217)Ggc>Agc	p.G739S	RP11-737O24.5_ENST00000608032.1_RNA	NM_014646.2	NP_055461.1	Q92539	LPIN2_HUMAN	lipin 2	739	C-LIP.				cellular lipid metabolic process (GO:0044255)|dephosphorylation (GO:0016311)|fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|lipid metabolic process (GO:0006629)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride biosynthetic process (GO:0019432)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)|transcription coactivator activity (GO:0003713)			autonomic_ganglia(1)|breast(1)|endometrium(2)|large_intestine(4)|lung(16)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	29				READ - Rectum adenocarcinoma(2;0.0419)|Colorectal(6;0.156)		TCGGCCATGCCGATGGCACGA	0.542																																						ENST00000261596.4																			0				autonomic_ganglia(1)|breast(1)|endometrium(2)|large_intestine(4)|lung(16)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	29						c.(2215-2217)Ggc>Agc		lipin 2							40.0	43.0	42.0					18																	2922157		2203	4300	6503	SO:0001583	missense	9663				fatty acid metabolic process|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent|triglyceride biosynthetic process	cytosol|endoplasmic reticulum membrane|nucleus	phosphatidate phosphatase activity|transcription coactivator activity	g.chr18:2922157C>T	D87436	CCDS11829.1	18p	2014-09-17			ENSG00000101577	ENSG00000101577			14450	protein-coding gene	gene with protein product		605519				11138012, 9039502	Standard	NM_014646		Approved	KIAA0249	uc002klo.3	Q92539	OTTHUMG00000131508	ENST00000261596.4:c.2215G>A	18.37:g.2922157C>T	ENSP00000261596:p.Gly739Ser						p.G739S	NM_014646.2	NP_055461.1	Q92539	LPIN2_HUMAN		READ - Rectum adenocarcinoma(2;0.0419)|Colorectal(6;0.156)	17	2453	-			739			C-LIP.		A7MD25|D3DUH3	Missense_Mutation	SNP	ENST00000261596.4	37	c.2215G>A	CCDS11829.1	.	.	.	.	.	.	.	.	.	.	C	36	5.852247	0.97023	.	.	ENSG00000101577	ENST00000261596	T	0.78126	-1.15	5.69	5.69	0.88448	HAD-like domain (2);LNS2, Lipin/Ned1/Smp2 (2);	0.000000	0.85682	D	0.000000	T	0.82038	0.4950	M	0.64080	1.96	0.80722	D	1	D	0.59767	0.986	P	0.50378	0.639	T	0.80618	-0.1302	10	0.36615	T	0.2	-24.9133	19.8167	0.96571	0.0:1.0:0.0:0.0	.	739	Q92539	LPIN2_HUMAN	S	739	ENSP00000261596:G739S	ENSP00000261596:G739S	G	-	1	0	LPIN2	2912157	1.000000	0.71417	0.993000	0.49108	0.961000	0.63080	7.398000	0.79919	2.679000	0.91253	0.563000	0.77884	GGC		0.542	LPIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254363.2	NM_014646		6	232	0	0	0	1	0	6	232				
GPR42	2866	broad.mit.edu	37	19	35862781	35862781	+	Missense_Mutation	SNP	T	T	C	rs424241	byFrequency	TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr19:35862781T>C	ENST00000454971.1	+	2	721	c.520T>C	c.(520-522)Tgg>Cgg	p.W174R	GPR42_ENST00000597214.1_Missense_Mutation_p.W174R			O15529	GPR42_HUMAN	G protein-coupled receptor 42 (gene/pseudogene)	174			W -> R (restores responses to propionate). {ECO:0000269|PubMed:19630535}.			integral component of plasma membrane (GO:0005887)	signal transducer activity (GO:0004871)			endometrium(1)|kidney(1)|skin(2)	4	all_lung(56;9.78e-09)|Lung NSC(56;1.46e-08)|Esophageal squamous(110;0.162)		Epithelial(14;1.29e-19)|OV - Ovarian serous cystadenocarcinoma(14;4.63e-18)|all cancers(14;5.19e-17)|LUSC - Lung squamous cell carcinoma(66;0.0221)			CCTGGAGTTCTGGAAGGACCA	0.597													C|||	1400	0.279553	0.2897	0.1816	5008	,	,		4948	0.5526		0.16	False		,,,				2504	0.1769					ENST00000454971.1																			0				endometrium(1)|kidney(1)|skin(2)	4						c.(520-522)Tgg>Cgg		G protein-coupled receptor 42 (gene/pseudogene)							22.0	26.0	25.0					19																	35862781		978	2469	3447	SO:0001583	missense	2866							g.chr19:35862781T>C	AF024689		19q13.12	2012-08-20	2010-02-09	2010-02-09	ENSG00000126251	ENSG00000126251		"""GPCR / Class A : Fatty acid receptors"""	4500	protein-coding gene	gene with protein product		603822	"""G protein-coupled receptor 42 pseudogene"""	GPR42P		9344866, 19630535	Standard	NG_008348		Approved	GPR41L, FFAR3L		O15529	OTTHUMG00000157124	ENST00000454971.1:c.520T>C	19.37:g.35862781T>C	ENSP00000410925:p.Trp174Arg					GPR42_ENST00000597214.1_Missense_Mutation_p.W174R	p.W174R					Epithelial(14;1.29e-19)|OV - Ovarian serous cystadenocarcinoma(14;4.63e-18)|all cancers(14;5.19e-17)|LUSC - Lung squamous cell carcinoma(66;0.0221)		2	721	+	all_lung(56;9.78e-09)|Lung NSC(56;1.46e-08)|Esophageal squamous(110;0.162)								Missense_Mutation	SNP	ENST00000454971.1	37	c.520T>C		.	.	.	.	.	.	.	.	.	.	C	0.614	-0.823929	0.02755	.	.	ENSG00000126251	ENST00000454971	T	0.37058	1.22	4.27	-3.16	0.05217	GPCR, rhodopsin-like superfamily (1);	0.716557	0.11750	N	0.533096	T	0.12433	0.0302	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.28964	-1.0027	8	0.11794	T	0.64	-3.6478	0.1462	0.00088	0.2586:0.2147:0.2545:0.2721	.	174	O15529	GPR42_HUMAN	R	174	ENSP00000410925:W174R	ENSP00000410925:W174R	W	+	1	0	GPR42	40554621	0.000000	0.05858	0.051000	0.19133	0.002000	0.02628	-1.480000	0.02325	-0.259000	0.09432	-0.186000	0.12905	TGG		0.597	GPR42-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000347518.1	NM_005305		7	131	0	0	0	1	0	7	131				
CHEK2	11200	broad.mit.edu	37	22	29091841	29091841	+	Silent	SNP	G	G	A	rs146546850	byFrequency	TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr22:29091841G>A	ENST00000405598.1	-	12	1307	c.1116C>T	c.(1114-1116)tcC>tcT	p.S372S	CHEK2_ENST00000464581.1_5'Flank|CHEK2_ENST00000382580.2_Silent_p.S415S|CHEK2_ENST00000544772.1_Silent_p.S151S|CHEK2_ENST00000382566.1_3'UTR|CHEK2_ENST00000382578.1_Silent_p.S281S|CHEK2_ENST00000328354.6_Silent_p.S372S|CHEK2_ENST00000382565.1_Intron|CHEK2_ENST00000402731.1_Silent_p.S343S|CHEK2_ENST00000404276.1_Silent_p.S372S|CHEK2_ENST00000403642.1_Silent_p.S281S|CHEK2_ENST00000348295.3_Silent_p.S343S			O96017	CHK2_HUMAN	checkpoint kinase 2	372	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.|T-loop/activation segment.				cellular protein catabolic process (GO:0044257)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|double-strand break repair (GO:0006302)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|replicative senescence (GO:0090399)|response to gamma radiation (GO:0010332)|signal transduction in response to DNA damage (GO:0042770)|signal transduction involved in intra-S DNA damage checkpoint (GO:0072428)|spindle assembly involved in mitosis (GO:0090307)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|PML body (GO:0016605)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)	p.S372S(8)		central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						CCAAAATCTTGGAGTGCCCAA	0.413			F			breast		Direct reversal of damage;Other conserved DNA damage response genes																														ENST00000544772.1			yes	Rec		familial breast cancer	22	22q12.1	11200	F	CHK2 checkpoint homolog (S. pombe)			E		breast			8	Substitution - coding silent(8)	p.S372S(8)	kidney(4)|prostate(2)|endometrium(1)|central_nervous_system(1)	central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						c.(451-453)tcC>tcT	Direct reversal of damage;Other conserved DNA damage response genes	checkpoint kinase 2							43.0	44.0	44.0					22																	29091841		2203	4300	6503	SO:0001819	synonymous_variant	11200				cell cycle|DNA damage checkpoint|DNA damage response, signal transduction resulting in induction of apoptosis|replicative senescence	PML body	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity	g.chr22:29091841G>A	AF086904	CCDS13843.1, CCDS13844.1, CCDS33629.1	22q12.1	2014-09-17	2011-11-11	2001-09-27	ENSG00000183765	ENSG00000183765			16627	protein-coding gene	gene with protein product		604373	"""CHK2 (checkpoint, S.pombe) homolog"", ""CHK2 checkpoint homolog (S. pombe)"""	RAD53		9836640, 10097108	Standard	NM_001257387		Approved	CDS1, CHK2, HuCds1, PP1425, bA444G7	uc003adt.1	O96017	OTTHUMG00000151023	ENST00000405598.1:c.1116C>T	22.37:g.29091841G>A						CHEK2_ENST00000382566.1_3'UTR|CHEK2_ENST00000402731.1_Silent_p.S343S|CHEK2_ENST00000348295.3_Silent_p.S343S|CHEK2_ENST00000382580.2_Silent_p.S415S|CHEK2_ENST00000328354.6_Silent_p.S372S|CHEK2_ENST00000382565.1_Intron|CHEK2_ENST00000404276.1_Silent_p.S372S|CHEK2_ENST00000405598.1_Silent_p.S372S|CHEK2_ENST00000382578.1_Silent_p.S281S|CHEK2_ENST00000403642.1_Silent_p.S281S	p.S151S	NM_001257387.1	NP_001244316.1	O96017	CHK2_HUMAN			12	1889	-			372			FHA.		A8K3Y9|B7ZBF3|B7ZBF4|B7ZBF5|Q6QA03|Q6QA04|Q6QA05|Q6QA06|Q6QA07|Q6QA08|Q6QA10|Q6QA11|Q6QA12|Q6QA13|Q9HBS5|Q9HCQ8|Q9UGF0|Q9UGF1	Silent	SNP	ENST00000405598.1	37	c.453C>T	CCDS13843.1	.	.	.	.	.	.	.	.	.	.	G	5.792	0.330417	0.10956	.	.	ENSG00000183765	ENST00000434810	.	.	.	5.89	-2.11	0.07187	.	.	.	.	.	T	0.42154	0.1190	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.33854	-0.9852	4	.	.	.	-7.6356	3.2532	0.06822	0.327:0.1103:0.4613:0.1014	.	.	.	.	L	116	.	.	P	-	2	0	CHEK2	27421841	0.997000	0.39634	0.996000	0.52242	0.470000	0.32858	0.318000	0.19504	-0.075000	0.12798	-0.907000	0.02831	CCA		0.413	CHEK2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321150.1	NM_001005735		9	311	0	0	0	1	0	9	311				
PCBP3	54039	broad.mit.edu	37	21	47333995	47333995	+	Intron	SNP	A	A	C			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr21:47333995A>C	ENST00000400314.1	+	10	1013				PCBP3_ENST00000400304.1_Missense_Mutation_p.H212P|PCBP3_ENST00000400310.1_Intron|PCBP3_ENST00000400308.1_Intron|PCBP3_ENST00000449640.1_Intron|PCBP3_ENST00000400309.1_Intron			P57721	PCBP3_HUMAN	poly(rC) binding protein 3						mRNA metabolic process (GO:0016071)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			biliary_tract(1)|endometrium(3)|large_intestine(2)|lung(7)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	17	all_hematologic(128;0.24)			Colorectal(79;0.0411)|READ - Rectum adenocarcinoma(84;0.0649)		TTACTGCAGCACCCGCCGCTG	0.627																																						ENST00000400304.1																			0				biliary_tract(1)|endometrium(3)|large_intestine(2)|lung(7)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	17						c.(634-636)cAc>cCc		poly(rC) binding protein 3							17.0	24.0	22.0					21																	47333995		691	1589	2280	SO:0001627	intron_variant	54039				mRNA metabolic process	cytosol|mitochondrion|nucleus|ribonucleoprotein complex	DNA binding|RNA binding	g.chr21:47333995A>C	AF176329	CCDS42974.2, CCDS46652.1	21q22.3	2013-07-16	2001-11-28		ENSG00000183570	ENSG00000183570			8651	protein-coding gene	gene with protein product		608502	"""poly(rC)-binding protein 3"""			10936052	Standard	NM_020528		Approved		uc002zhq.2	P57721	OTTHUMG00000090399	ENST00000400314.1:c.675+56A>C	21.37:g.47333995A>C						PCBP3_ENST00000400308.1_Intron|PCBP3_ENST00000400314.1_Intron|PCBP3_ENST00000468429.1_Intron|PCBP3_ENST00000400309.1_Intron|PCBP3_ENST00000400310.1_Intron|PCBP3_ENST00000449640.1_Intron	p.H212P			P57721	PCBP3_HUMAN		Colorectal(79;0.0411)|READ - Rectum adenocarcinoma(84;0.0649)	7	635	+	all_hematologic(128;0.24)		225					A8MPS2|A8MQ26|B7WNN9|B7WPC1|Q8N9K6|Q96EP6	Missense_Mutation	SNP	ENST00000400314.1	37	c.635A>C	CCDS42974.2	.	.	.	.	.	.	.	.	.	.	A	11.01	1.513211	0.27123	.	.	ENSG00000183570	ENST00000400304	T	0.48522	0.81	4.95	2.7	0.31948	.	0.165376	0.24041	U	0.042092	T	0.33527	0.0866	.	.	.	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.07462	-1.0771	9	0.35671	T	0.21	.	7.244	0.26112	0.741:0.1764:0.0826:0.0	.	212	E9PFP8	.	P	212	ENSP00000383159:H212P	ENSP00000383159:H212P	H	+	2	0	PCBP3	46158423	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.683000	0.68189	0.324000	0.23333	0.460000	0.39030	CAC		0.627	PCBP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206808.2			37	132	0	0	0	1	0	37	132				
NCOA6	23054	broad.mit.edu	37	20	33345744	33345744	+	Silent	SNP	C	C	T			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr20:33345744C>T	ENST00000374796.2	-	8	3377	c.807G>A	c.(805-807)caG>caA	p.Q269Q	NCOA6_ENST00000359003.2_Silent_p.Q269Q			Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	269	CREBBP-binding region.|Gln-rich.|NCOA1-binding region.|TBP/GTF2A-binding region.				brain development (GO:0007420)|cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-templated transcription, initiation (GO:0006352)|glucocorticoid receptor signaling pathway (GO:0042921)|heart development (GO:0007507)|intracellular estrogen receptor signaling pathway (GO:0030520)|labyrinthine layer blood vessel development (GO:0060716)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)	histone methyltransferase complex (GO:0035097)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)	p.Q269Q(15)		NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(8)|large_intestine(16)|lung(37)|ovary(4)|prostate(5)|skin(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	107						gctgctgctgctgttgttgtt	0.537																																						ENST00000374796.2																			15	Substitution - coding silent(15)	p.Q269Q(15)	lung(5)|prostate(4)|endometrium(3)|central_nervous_system(1)|urinary_tract(1)|kidney(1)	NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(8)|large_intestine(16)|lung(37)|ovary(4)|prostate(5)|skin(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	107						c.(805-807)caG>caA		nuclear receptor coactivator 6							64.0	52.0	56.0					20																	33345744		2203	4300	6503	SO:0001819	synonymous_variant	23054				brain development|cellular lipid metabolic process|DNA recombination|DNA repair|DNA replication|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|heart development|myeloid cell differentiation|positive regulation of transcription from RNA polymerase II promoter|response to hormone stimulus|transcription initiation from RNA polymerase II promoter	transcription factor complex	chromatin binding|enzyme binding|estrogen receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|retinoid X receptor binding|thyroid hormone receptor binding	g.chr20:33345744C>T	AF128458	CCDS13241.1, CCDS74720.1	20q11	2008-08-01			ENSG00000198646	ENSG00000198646			15936	protein-coding gene	gene with protein product	"""nuclear receptor coactivator RAP250"", ""activating signal cointegrator-2"", ""peroxisome proliferator-activated receptor interacting protein"""	605299				8724849, 8263591	Standard	NM_014071		Approved	KIAA0181, RAP250, ASC2, AIB3, PRIP, TRBP, NRC	uc002xaw.3	Q14686	OTTHUMG00000032311	ENST00000374796.2:c.807G>A	20.37:g.33345744C>T						NCOA6_ENST00000359003.2_Silent_p.Q269Q	p.Q269Q			Q14686	NCOA6_HUMAN			8	3377	-			269			CREBBP-binding region.|Gln-rich.|NCOA1-binding region.|TBP/GTF2A-binding region.		A6NLF1|B2RMN5|E1P5P7|Q9NTZ9|Q9UH74|Q9UK86	Silent	SNP	ENST00000374796.2	37	c.807G>A	CCDS13241.1																																																																																				0.537	NCOA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078811.2	NM_014071		9	239	0	0	0	1	0	9	239				
LRRC37A4P	55073	broad.mit.edu	37	17	43587569	43587569	+	RNA	SNP	G	G	C	rs202189074		TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr17:43587569G>C	ENST00000579913.1	-	0	1444				RP11-798G7.5_ENST00000253803.2_RNA	NR_002940.2				leucine rich repeat containing 37, member A4, pseudogene																		aactccgtctgaaaagaaaag	0.443																																						ENST00000253803.2																			0																																																			0							g.chr17:43587569G>C	AK000982		17q21.31	2014-04-01	2012-03-07	2012-03-07	ENSG00000214425	ENSG00000214425			25479	pseudogene	pseudogene			"""leucine rich repeat containing 37, member A4 (pseudogene)"""	LRRC37A4			Standard	NR_002940		Approved	FLJ10120	uc031rhd.1		OTTHUMG00000179212		17.37:g.43587569G>C						LRRC37A4P_ENST00000579913.1_RNA								0	267	+									RNA	SNP	ENST00000579913.1	37																																																																																						0.443	LRRC37A4P-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000445300.1	NR_002940		7	131	0	0	0	1	0	7	131				
FOXP2	93986	broad.mit.edu	37	7	114270000	114270000	+	Silent	SNP	G	G	A			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr7:114270000G>A	ENST00000393494.2	+	5	816	c.537G>A	c.(535-537)caG>caA	p.Q179Q	FOXP2_ENST00000390668.3_Silent_p.Q203Q|AC020606.1_ENST00000580664.1_RNA|FOXP2_ENST00000350908.4_Silent_p.Q179Q|FOXP2_ENST00000393498.2_Silent_p.Q159Q|FOXP2_ENST00000403559.4_Silent_p.Q196Q|FOXP2_ENST00000408937.3_Silent_p.Q204Q|FOXP2_ENST00000393491.3_Silent_p.Q87Q|FOXP2_ENST00000393500.3_Silent_p.Q104Q|FOXP2_ENST00000360232.4_Silent_p.Q179Q|FOXP2_ENST00000378237.3_Silent_p.Q179Q|FOXP2_ENST00000393489.3_Silent_p.Q87Q			O15409	FOXP2_HUMAN	forkhead box P2	179	Gln-rich.				camera-type eye development (GO:0043010)|caudate nucleus development (GO:0021757)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|growth (GO:0040007)|lung alveolus development (GO:0048286)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of mesenchymal cell proliferation (GO:0002053)|post-embryonic development (GO:0009791)|putamen development (GO:0021758)|righting reflex (GO:0060013)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|vocal learning (GO:0042297)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|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)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Q204Q(1)		breast(3)|endometrium(7)|kidney(4)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	52						agcaacaacagcagcagcagc	0.498																																						ENST00000393500.3																			1	Substitution - coding silent(1)	p.Q204Q(1)	lung(1)	breast(3)|endometrium(7)|kidney(4)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	52						c.(310-312)caG>caA		forkhead box P2							41.0	38.0	39.0					7																	114270000		2199	4282	6481	SO:0001819	synonymous_variant	93986				camera-type eye development|caudate nucleus development|cerebellum development|cerebral cortex development|embryo development|growth|lung alveolus development|negative regulation of transcription, DNA-dependent|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of mesenchymal cell proliferation|post-embryonic development|putamen development|regulation of sequence-specific DNA binding transcription factor activity|righting reflex|skeletal muscle tissue development|smooth muscle tissue development|vocal learning	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding	g.chr7:114270000G>A	U80741	CCDS5760.1, CCDS5761.1, CCDS43635.1, CCDS5761.2, CCDS55154.1	7q31	2008-07-18			ENSG00000128573	ENSG00000128573		"""Forkhead boxes"""	13875	protein-coding gene	gene with protein product	"""trinucleotide repeat containing 10"", ""forkhead/winged-helix transcription factor"", ""speech and language disorder 1"", ""CAG repeat protein 44"""	605317		TNRC10, SPCH1		11586359, 9225980	Standard	NM_014491		Approved	CAGH44	uc003vgz.3	O15409	OTTHUMG00000023131	ENST00000393494.2:c.537G>A	7.37:g.114270000G>A						FOXP2_ENST00000393489.3_Silent_p.Q87Q|FOXP2_ENST00000393491.3_Silent_p.Q87Q|FOXP2_ENST00000393494.2_Silent_p.Q179Q|FOXP2_ENST00000378237.3_Silent_p.Q179Q|FOXP2_ENST00000350908.4_Silent_p.Q179Q|FOXP2_ENST00000390668.3_Silent_p.Q203Q|FOXP2_ENST00000360232.4_Silent_p.Q179Q|FOXP2_ENST00000408937.3_Silent_p.Q204Q|AC020606.1_ENST00000580664.1_RNA|FOXP2_ENST00000403559.4_Silent_p.Q196Q|FOXP2_ENST00000393498.2_Silent_p.Q159Q	p.Q104Q			O15409	FOXP2_HUMAN			11	1132	+			179			Gln-rich.		A0AUV6|A4D0U8|A6NNW4|B4DLD9|Q6ZND1|Q75MJ3|Q8IZE0|Q8N0W2|Q8N6B7|Q8N6B8|Q8NFQ1|Q8NFQ2|Q8NFQ3|Q8NFQ4|Q8TD74	Silent	SNP	ENST00000393494.2	37	c.312G>A	CCDS5760.1																																																																																				0.498	FOXP2-014	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317366.1	NM_014491		9	356	0	0	0	1	0	9	356				
VAMP3	9341	broad.mit.edu	37	1	7838212	7838214	+	In_Frame_Del	DEL	TCA	TCA	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr1:7838212_7838214delTCA	ENST00000054666.6	+	4	381_383	c.266_268delTCA	c.(265-270)ttcatc>ttc	p.I94del	RP3-467L1.6_ENST00000602406.1_RNA|VAMP3_ENST00000470357.1_In_Frame_Del_p.I66del	NM_004781.3	NP_004772.1	Q15836	VAMP3_HUMAN	vesicle-associated membrane protein 3	94					calcium ion-dependent exocytosis (GO:0017156)|exocytosis (GO:0006887)|Golgi to plasma membrane protein transport (GO:0043001)|membrane fusion (GO:0061025)|positive regulation of receptor recycling (GO:0001921)|protein complex assembly (GO:0006461)|retrograde transport, endosome to Golgi (GO:0042147)|SNARE complex assembly (GO:0035493)|substrate adhesion-dependent cell spreading (GO:0034446)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|cell junction (GO:0030054)|cell surface (GO:0009986)|clathrin-coated vesicle (GO:0030136)|clathrin-coated vesicle membrane (GO:0030665)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)|secretory granule (GO:0030141)|SNARE complex (GO:0031201)|synapse (GO:0045202)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)	6	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;9.35e-21)|all_lung(118;7.57e-07)|Lung NSC(185;4.52e-06)|Renal(390;0.000147)|Breast(487;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;6.33e-69)|GBM - Glioblastoma multiforme(8;2.07e-34)|Colorectal(212;1.36e-07)|COAD - Colon adenocarcinoma(227;1.38e-05)|Kidney(185;4.89e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000805)|KIRC - Kidney renal clear cell carcinoma(229;0.000917)|STAD - Stomach adenocarcinoma(132;0.000985)|READ - Rectum adenocarcinoma(331;0.0642)		CTGGTTATCTTCATCATCATCAT	0.365																																						ENST00000054666.6																			0				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)	6						c.(265-270)ttc>t		vesicle-associated membrane protein 3																																				SO:0001651	inframe_deletion	9341				cellular membrane fusion|positive regulation of receptor recycling|protein complex assembly|protein transport|retrograde transport, endosome to Golgi|substrate adhesion-dependent cell spreading|vesicle docking involved in exocytosis	cell junction|clathrin-coated vesicle|integral to membrane|recycling endosome|synapse|synaptosome	protein binding	g.chr1:7838212_7838214delTCA	BC003570	CCDS88.1	1p36.23	2013-02-13	2012-10-17		ENSG00000049245	ENSG00000049245		"""Vesicle-associated membrane proteins"""	12644	protein-coding gene	gene with protein product	"""cellubrevin"""	603657				9885218	Standard	NM_004781		Approved	CEB	uc001aol.3	Q15836	OTTHUMG00000001225	ENST00000054666.6:c.266_268delTCA	1.37:g.7838221_7838223delTCA	ENSP00000054666:p.Ile94del					VAMP3_ENST00000470357.1_In_Frame_Del_p.FI61del	p.FI89del	NM_004781.3	NP_004772.1	Q15836	VAMP3_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;6.33e-69)|GBM - Glioblastoma multiforme(8;2.07e-34)|Colorectal(212;1.36e-07)|COAD - Colon adenocarcinoma(227;1.38e-05)|Kidney(185;4.89e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000805)|KIRC - Kidney renal clear cell carcinoma(229;0.000917)|STAD - Stomach adenocarcinoma(132;0.000985)|READ - Rectum adenocarcinoma(331;0.0642)	4	381_383	+	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;9.35e-21)|all_lung(118;7.57e-07)|Lung NSC(185;4.52e-06)|Renal(390;0.000147)|Breast(487;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)	89					Q9BRV4	In_Frame_Del	DEL	ENST00000054666.6	37	c.266_268delTCA	CCDS88.1																																																																																				0.365	VAMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003625.1	NM_004781		7	984						7	984	---	---	---	---
ESPNP	284729	broad.mit.edu	37	1	17034125	17034126	+	RNA	INS	-	-	AGCT	rs141324796|rs79472512	byFrequency	TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr1:17034125_17034126insAGCT	ENST00000492551.1	-	0	477_478					NR_026567.1				espin pseudogene																		CAGCAGCAGCCAGCTGAGCACC	0.718														1500	0.299521	0.1188	0.3444	5008	,	,		24180	0.4177		0.3101	False		,,,				2504	0.3793					ENST00000492551.1																			0																																																			0							g.chr1:17034125_17034126insAGCT	AL035288		1p36.13	2013-05-22			ENSG00000268869	ENSG00000268869			23285	pseudogene	pseudogene						15286153	Standard	NR_026567		Approved		uc001azn.1		OTTHUMG00000000803		1.37:g.17034126_17034129dupAGCT								NR_026567.1						0	477_478	-									RNA	INS	ENST00000492551.1	37																																																																																						0.718	ESPNP-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000326311.1			12	28						12	28	---	---	---	---
CCDC28B	79140	broad.mit.edu	37	1	32670247	32670248	+	Intron	DEL	TG	TG	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr1:32670247_32670248delTG	ENST00000373602.5	+	5	895				RP4-622L5.7_ENST00000373604.4_RNA|CCDC28B_ENST00000421922.2_Frame_Shift_Del_p.C192fs|CCDC28B_ENST00000483009.1_Intron|RP4-622L5.7_ENST00000421616.1_RNA|IQCC_ENST00000291358.6_5'Flank|IQCC_ENST00000537469.1_5'Flank	NM_024296.3	NP_077272.2	Q9BUN5	CC28B_HUMAN	coiled-coil domain containing 28B						cilium assembly (GO:0042384)	centrosome (GO:0005813)|cytoplasm (GO:0005737)				large_intestine(4)|lung(3)|ovary(1)|upper_aerodigestive_tract(2)	10		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.174)				AACCCGTCTATGTGTGTGTGTT	0.5																																						ENST00000421922.2																			0				large_intestine(4)|lung(3)|ovary(1)|upper_aerodigestive_tract(2)	10						c.(574-576)tfs		coiled-coil domain containing 28B																																				SO:0001627	intron_variant	79140							g.chr1:32670247_32670248delTG	BC022848	CCDS354.2, CCDS72749.1	1p36.11-p34.2	2008-02-05			ENSG00000160050	ENSG00000160050			28163	protein-coding gene	gene with protein product		610162				16327777	Standard	XM_006710892		Approved	MGC1203, RP4-622L5.5	uc001bul.1	Q9BUN5	OTTHUMG00000005738	ENST00000373602.5:c.548+26TG>-	1.37:g.32670255_32670256delTG						CCDC28B_ENST00000373602.5_Intron|CCDC28B_ENST00000483009.1_Intron	p.C192fs			Q9BUN5	CC28B_HUMAN			5	674_675	+		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.174)	0					A8K789|Q8TBV8	Frame_Shift_Del	DEL	ENST00000373602.5	37	c.574_575delTG	CCDS354.2																																																																																				0.500	CCDC28B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015723.4	NM_024296		13	1200						13	1200	---	---	---	---
ZBTB8A	653121	broad.mit.edu	37	1	33065979	33065981	+	In_Frame_Del	DEL	GAA	GAA	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr1:33065979_33065981delGAA	ENST00000373510.4	+	5	1514_1516	c.1285_1287delGAA	c.(1285-1287)gaadel	p.E433del	ZBTB8OS_ENST00000341885.5_Intron|RP1-27O5.3_ENST00000480336.1_3'UTR|ZBTB8A_ENST00000316459.4_3'UTR	NM_001040441.1	NP_001035531.1	Q96BR9	ZBT8A_HUMAN	zinc finger and BTB domain containing 8A	433	Poly-Glu.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(2)|large_intestine(2)|lung(2)|prostate(1)	7						TGATGATAGTGAAGAAGAAGAAG	0.414																																						ENST00000373510.4																			0				cervix(2)|large_intestine(2)|lung(2)|prostate(1)	7						c.(1285-1287)del		zinc finger and BTB domain containing 8A				3,6,4257		0,0,3,0,6,2124						1.9	1.0			101	0,20,8234		0,0,0,0,20,4107	no	codingComplex	ZBTB8A	NM_001040441.1		0,0,3,0,26,6231	A1A1,A1A2,A1R,A2A2,A2R,RR		0.2423,0.211,0.2316				3,26,12491				SO:0001651	inframe_deletion	653121				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr1:33065979_33065981delGAA	AF548353	CCDS30664.1	1p34.3	2013-01-08	2009-03-25	2009-03-25	ENSG00000160062	ENSG00000160062		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	24172	protein-coding gene	gene with protein product			"""zinc finger and BTB domain containing 8"""	ZBTB8		12477932	Standard	NM_001040441		Approved	BOZF1, FLJ90065, ZNF916A	uc001bvn.3	Q96BR9	OTTHUMG00000007855	ENST00000373510.4:c.1285_1287delGAA	1.37:g.33065988_33065990delGAA	ENSP00000362609:p.Glu433del					ZBTB8OS_ENST00000341885.5_Intron|RP1-27O5.3_ENST00000480336.1_3'UTR|ZBTB8A_ENST00000316459.4_3'UTR	p.E433del	NM_001040441.1	NP_001035531.1	Q96BR9	ZBT8A_HUMAN			5	1514_1516	+			433			Poly-Glu.		Q8IUL5|Q8IWR9|Q8N2Y5|Q96BX0	In_Frame_Del	DEL	ENST00000373510.4	37	c.1285_1287delGAA	CCDS30664.1																																																																																				0.414	ZBTB8A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021665.2	NM_144621		7	418						7	418	---	---	---	---
PTPRF	5792	broad.mit.edu	37	1	44071946	44071948	+	In_Frame_Del	DEL	GCG	GCG	-	rs549143666|rs377569778	byFrequency	TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr1:44071946_44071948delGCG	ENST00000359947.4	+	20	3859_3861	c.3519_3521delGCG	c.(3517-3522)cagcgg>cag	p.R1178del	PTPRF_ENST00000438120.1_In_Frame_Del_p.R1169del|PTPRF_ENST00000422171.2_In_Frame_Del_p.R526del|PTPRF_ENST00000372413.3_In_Frame_Del_p.R1169del|PTPRF_ENST00000372414.3_In_Frame_Del_p.R1178del|PTPRF_ENST00000496447.1_3'UTR	NM_002840.3	NP_002831.2	P10586	PTPRF_HUMAN	protein tyrosine phosphatase, receptor type, F	1178					cell adhesion (GO:0007155)|cell migration (GO:0016477)|negative regulation of receptor binding (GO:1900121)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	heparin binding (GO:0008201)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(2)|breast(4)|central_nervous_system(3)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(24)|ovary(4)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)	72	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				GAGAGGAGCAGCGGCGGCGGCGG	0.631																																						ENST00000359947.4																			0				NS(2)|breast(4)|central_nervous_system(3)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(24)|ovary(4)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)	72						c.(3517-3522)cag>ca		protein tyrosine phosphatase, receptor type, F																																				SO:0001651	inframe_deletion	5792				transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	transmembrane receptor protein tyrosine phosphatase activity	g.chr1:44071946_44071948delGCG	Y00815	CCDS489.2, CCDS490.2	1p34	2013-02-11			ENSG00000142949	ENSG00000142949		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9670	protein-coding gene	gene with protein product		179590		LAR		7558042	Standard	NM_130440		Approved		uc001cjr.3	P10586	OTTHUMG00000007501	ENST00000359947.4:c.3519_3521delGCG	1.37:g.44071955_44071957delGCG	ENSP00000353030:p.Arg1178del					PTPRF_ENST00000422171.2_In_Frame_Del_p.QR521del|PTPRF_ENST00000372413.3_In_Frame_Del_p.QR1164del|PTPRF_ENST00000372414.3_In_Frame_Del_p.QR1173del|PTPRF_ENST00000496447.1_3'UTR|PTPRF_ENST00000438120.1_In_Frame_Del_p.QR1164del	p.QR1173del	NM_002840.3	NP_002831.2	P10586	PTPRF_HUMAN			20	3859_3861	+	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)	1173					D3DPX6|D3DPX7|Q5T021|Q5T022|Q5W9G2|Q86WS0	In_Frame_Del	DEL	ENST00000359947.4	37	c.3519_3521delGCG	CCDS489.2																																																																																				0.631	PTPRF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000019710.1			11	778						11	778	---	---	---	---
SLC6A9	6536	broad.mit.edu	37	1	44489938	44489938	+	Frame_Shift_Del	DEL	T	T	-	rs201148088		TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr1:44489938delT	ENST00000372310.3	-	2	177	c.12delA	c.(10-12)aaafs	p.K4fs	SLC6A9_ENST00000475075.2_5'UTR|SLC6A9_ENST00000372306.3_Frame_Shift_Del_p.K4fs|SLC6A9_ENST00000537678.1_5'UTR|SLC6A9_ENST00000492434.2_5'UTR	NM_001024845.2	NP_001020016.1	P48067	SC6A9_HUMAN	solute carrier family 6 (neurotransmitter transporter, glycine), member 9	335					transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycine:sodium symporter activity (GO:0015375)|neurotransmitter:sodium symporter activity (GO:0005328)			endometrium(3)|large_intestine(8)|lung(7)|ovary(1)|skin(1)|urinary_tract(2)	22	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0511)			Glycine(DB00145)	CTTTGGCACCTTTTCCTACCA	0.627																																						ENST00000372310.3																			0				endometrium(3)|large_intestine(8)|lung(7)|ovary(1)|skin(1)|urinary_tract(2)	22						c.(10-12)aafs		solute carrier family 6 (neurotransmitter transporter, glycine), member 9	Glycine(DB00145)						231.0	218.0	222.0					1																	44489938		2203	4300	6503	SO:0001589	frameshift_variant	6536					integral to plasma membrane|membrane fraction	glycine:sodium symporter activity|neurotransmitter:sodium symporter activity	g.chr1:44489938delT	S70609	CCDS30695.1, CCDS41316.1, CCDS41317.1	1p33	2013-05-22			ENSG00000196517	ENSG00000196517		"""Solute carriers"""	11056	protein-coding gene	gene with protein product		601019				8183239, 7587377	Standard	NM_006934		Approved	GLYT1	uc001cll.4	P48067	OTTHUMG00000008294	ENST00000372310.3:c.12delA	1.37:g.44489938delT	ENSP00000361384:p.Lys4fs					SLC6A9_ENST00000537678.1_5'UTR|SLC6A9_ENST00000492434.2_5'UTR|SLC6A9_ENST00000372306.3_Frame_Shift_Del_p.K4fs|SLC6A9_ENST00000475075.2_5'UTR	p.K4fs	NM_001024845.2	NP_001020016.1	P48067	SC6A9_HUMAN			2	177	-	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0511)	335					A6NDH1|A6NII2|A6NNZ8|Q5TAB8|Q5TAB9|Q5TAC0	Frame_Shift_Del	DEL	ENST00000372310.3	37	c.12delA	CCDS30695.1																																																																																				0.627	SLC6A9-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022827.1	NM_201649		7	1830						7	1830	---	---	---	---
KRT8P47	644743	broad.mit.edu	37	1	44570056	44570058	+	lincRNA	DEL	CTG	CTG	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr1:44570056_44570058delCTG	ENST00000434244.1	+	0	2053_2055																											TCCCAGCCGTCTGCTGCTGCTGC	0.576																																						ENST00000434244.1																			0																																																			0							g.chr1:44570056_44570058delCTG																													1.37:g.44570065_44570067delCTG														0	2053_2055	+									RNA	DEL	ENST00000434244.1	37																																																																																						0.576	RP5-1198O20.4-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000022875.2			7	507						7	507	---	---	---	---
C1orf168	199920	broad.mit.edu	37	1	57192198	57192199	+	Frame_Shift_Ins	INS	-	-	T			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr1:57192198_57192199insT	ENST00000343433.6	-	16	1931_1932	c.1851_1852insA	c.(1849-1854)aaagagfs	p.E618fs	C1orf168_ENST00000484327.1_5'Flank	NM_001004303.4	NP_001004303.3	Q5VWT5	CA168_HUMAN	chromosome 1 open reading frame 168	618										NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(13)|ovary(3)|skin(6)|stomach(1)|urinary_tract(2)	46						CCGTTTTTCTCTTTTTTTTCCT	0.376																																						ENST00000343433.6																			0				NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(13)|ovary(3)|skin(6)|stomach(1)|urinary_tract(2)	46						c.(1849-1854)aaagaafs		chromosome 1 open reading frame 168				1,4265		0,1,2132						1.8	0.0			130	0,8254		0,0,4127	no	frameshift	C1orf168	NM_001004303.4		0,1,6259	A1A1,A1R,RR		0.0,0.0234,0.0080				1,12519				SO:0001589	frameshift_variant	199920							g.chr1:57192198_57192199insT	BX648439	CCDS30729.1	1p32.2	2011-02-22			ENSG00000187889	ENSG00000187889			27295	protein-coding gene	gene with protein product						14702039	Standard	NM_001004303		Approved	RP4-758N20.2, FLJ43208	uc001cym.4	Q5VWT5	OTTHUMG00000008281	ENST00000343433.6:c.1852dupA	1.37:g.57192206_57192206dupT	ENSP00000345972:p.Glu618fs						p.E618fs	NM_001004303.4	NP_001004303.3	Q5VWT5	CA168_HUMAN			16	1931_1932	-			618					Q63HM3|Q6ZUY6	Frame_Shift_Ins	INS	ENST00000343433.6	37	c.1851_1852insA	CCDS30729.1																																																																																				0.376	C1orf168-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022751.2	NM_001004303		8	584						8	584	---	---	---	---
JAK1	3716	broad.mit.edu	37	1	65306996	65306997	+	Frame_Shift_Ins	INS	-	-	T	rs202179869|rs375979659		TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr1:65306996_65306997insT	ENST00000342505.4	-	19	2828_2829	c.2580_2581insA	c.(2578-2583)aaaccafs	p.P861fs	JAK1_ENST00000465376.1_5'Flank	NM_002227.2	NP_002218.2	P23458	JAK1_HUMAN	Janus kinase 1	861					cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-2-mediated signaling pathway (GO:0038110)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to antibiotic (GO:0046677)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(48)|kidney(3)|large_intestine(8)|liver(2)|lung(19)|ovary(1)|prostate(12)|skin(1)|soft_tissue(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	120				BRCA - Breast invasive adenocarcinoma(111;0.0485)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	TCAGTTGCTGGTTTTTTTTCTG	0.47			Mis		ALL																																	ENST00000342505.4				Dom	yes		1	1p32.3-p31.3	3716	Mis	Janus kinase 1			L			ALL		0				breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(48)|kidney(3)|large_intestine(8)|liver(2)|lung(19)|ovary(1)|prostate(12)|skin(1)|soft_tissue(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	120						c.(2578-2583)aacagcfs		Janus kinase 1																																				SO:0001589	frameshift_variant	3716				interferon-gamma-mediated signaling pathway|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|response to antibiotic|type I interferon-mediated signaling pathway	cytoskeleton|cytosol|endomembrane system|membrane|nucleus	ATP binding|growth hormone receptor binding|non-membrane spanning protein tyrosine kinase activity	g.chr1:65306996_65306997insT	M64174	CCDS41346.1	1p32.3-p31.3	2009-07-10	2009-04-23		ENSG00000162434	ENSG00000162434	2.7.10.1		6190	protein-coding gene	gene with protein product		147795		JAK1B		1848670, 7698020	Standard	NM_002227		Approved	JAK1A, JTK3	uc001dbu.1	P23458	OTTHUMG00000009310	ENST00000342505.4:c.2581dupA	1.37:g.65307004_65307004dupT	ENSP00000343204:p.Pro861fs						p.NS860fs	NM_002227.2	NP_002218.2	P23458	JAK1_HUMAN		BRCA - Breast invasive adenocarcinoma(111;0.0485)	19	2828_2829	-			860					Q59GQ2|Q9UD26	Frame_Shift_Ins	INS	ENST00000342505.4	37	c.2580_2581insA	CCDS41346.1																																																																																				0.470	JAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025791.1	NM_002227		7	737						7	737	---	---	---	---
BRDT	676	broad.mit.edu	37	1	92447228	92447230	+	In_Frame_Del	DEL	AGC	AGC	-	rs375773077		TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr1:92447228_92447230delAGC	ENST00000362005.3	+	13	2336_2338	c.1918_1920delAGC	c.(1918-1920)agcdel	p.S648del	BRDT_ENST00000399546.2_In_Frame_Del_p.S648del|BRDT_ENST00000402388.1_In_Frame_Del_p.S648del|BRDT_ENST00000370389.2_In_Frame_Del_p.S575del|BRDT_ENST00000394530.3_In_Frame_Del_p.S602del	NM_001242805.1	NP_001229734	Q58F21	BRDT_HUMAN	bromodomain, testis-specific	648	Ser-rich.				cell differentiation (GO:0030154)|chromatin remodeling (GO:0006338)|histone displacement (GO:0001207)|male meiosis (GO:0007140)|male meiosis I (GO:0007141)|mRNA processing (GO:0006397)|positive regulation of transcription during meiosis (GO:0051039)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone binding (GO:0042393)|lysine-acetylated histone binding (GO:0070577)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(24)|ovary(1)|prostate(4)|skin(2)|stomach(2)|urinary_tract(2)	56		all_lung(203;0.00531)|Lung NSC(277;0.0194)		all cancers(265;0.0228)|Epithelial(280;0.133)		ACTGAGTGAGagcagcagcagca	0.419																																						ENST00000370389.2																			0				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(24)|ovary(1)|prostate(4)|skin(2)|stomach(2)|urinary_tract(2)	56						c.(1699-1701)del		bromodomain, testis-specific																																				SO:0001651	inframe_deletion	676				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein serine/threonine kinase activity|transcription coactivator activity	g.chr1:92447228_92447230delAGC	AF019085	CCDS735.1, CCDS55615.1, CCDS55616.1, CCDS72820.1	1p22.1	2010-12-23			ENSG00000137948	ENSG00000137948			1105	protein-coding gene	gene with protein product	"""cancer/testis antigen 9"""	602144				9367677	Standard	NM_001726		Approved	BRD6, CT9	uc010osz.2	Q58F21	OTTHUMG00000010113	ENST00000362005.3:c.1918_1920delAGC	1.37:g.92447237_92447239delAGC	ENSP00000354568:p.Ser648del					BRDT_ENST00000394530.3_In_Frame_Del_p.S602del|BRDT_ENST00000402388.1_In_Frame_Del_p.S648del|BRDT_ENST00000362005.3_In_Frame_Del_p.S648del|BRDT_ENST00000399546.2_In_Frame_Del_p.S648del	p.S575del	NM_001242810.1	NP_001229739.1	Q58F21	BRDT_HUMAN		all cancers(265;0.0228)|Epithelial(280;0.133)	12	2623_2625	+		all_lung(203;0.00531)|Lung NSC(277;0.0194)	648					A6NF68|B7Z811|B7Z890|B7ZAX7|D3DT32|O14789|Q05DQ4|Q6P5T1|Q7Z4A6|Q8IWI6	In_Frame_Del	DEL	ENST00000362005.3	37	c.1699_1701delAGC	CCDS735.1																																																																																				0.419	BRDT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027980.2	NM_207189		11	564						11	564	---	---	---	---
TCHH	7062	broad.mit.edu	37	1	152082957	152082959	+	In_Frame_Del	DEL	CTC	CTC	-	rs143222885	byFrequency	TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr1:152082957_152082959delCTC	ENST00000368804.1	-	2	2733_2735	c.2734_2736delGAG	c.(2734-2736)gagdel	p.E912del		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	912	10 X 30 AA tandem repeats.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTCTCTGTAGCTCCTCCTCCTCC	0.586																																						ENST00000368804.1																			0				NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105						c.(2734-2736)del		trichohyalin																																				SO:0001651	inframe_deletion	7062				keratinization	cytoskeleton	calcium ion binding	g.chr1:152082957_152082959delCTC	L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"""EF-hand domain containing"""	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.2734_2736delGAG	1.37:g.152082966_152082968delCTC	ENSP00000357794:p.Glu912del						p.E912del	NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	LUSC - Lung squamous cell carcinoma(543;0.206)		2	2733_2735	-	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		912			10 X 30 AA tandem repeats.		Q5VUI3	In_Frame_Del	DEL	ENST00000368804.1	37	c.2734_2736delGAG	CCDS41396.1																																																																																				0.586	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113		19	1287						19	1287	---	---	---	---
CD1D	912	broad.mit.edu	37	1	158151257	158151257	+	Frame_Shift_Del	DEL	T	T	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr1:158151257delT	ENST00000368171.3	+	3	573	c.74delT	c.(73-75)cttfs	p.L25fs		NM_001766.3	NP_001757.1	P15813	CD1D_HUMAN	CD1d molecule	25					antigen processing and presentation, endogenous lipid antigen via MHC class Ib (GO:0048006)|detection of bacterium (GO:0016045)|heterotypic cell-cell adhesion (GO:0034113)|innate immune response (GO:0045087)|positive regulation of innate immune response (GO:0045089)|positive regulation of T cell proliferation (GO:0042102)|T cell selection (GO:0045058)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	beta-2-microglobulin binding (GO:0030881)|cell adhesion molecule binding (GO:0050839)|exogenous lipid antigen binding (GO:0030884)|histone binding (GO:0042393)|lipid antigen binding (GO:0030882)|receptor activity (GO:0004872)			endometrium(1)|kidney(2)|large_intestine(2)|lung(19)|ovary(1)|prostate(3)|urinary_tract(2)	30	all_hematologic(112;0.0378)					CCGCAAAGGCTTTTCCCCCTC	0.592																																						ENST00000368171.3																			0				endometrium(1)|kidney(2)|large_intestine(2)|lung(19)|ovary(1)|prostate(3)|urinary_tract(2)	30						c.(73-75)ctfs		CD1d molecule							202.0	226.0	218.0					1																	158151257		2203	4300	6503	SO:0001589	frameshift_variant	912				antigen processing and presentation, endogenous lipid antigen via MHC class Ib|detection of bacterium|innate immune response|interspecies interaction between organisms|positive regulation of innate immune response|T cell selection	endosome membrane|integral to plasma membrane|lysosomal membrane	beta-2-microglobulin binding|exogenous lipid antigen binding|histone binding	g.chr1:158151257delT	BC027926	CCDS1173.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158473	ENSG00000158473		"""CD molecules"", ""Immunoglobulin superfamily / C1-set domain containing"""	1637	protein-coding gene	gene with protein product		188410	"""CD1D antigen, d polypeptide"", ""CD1d antigen"""			2463622	Standard	NM_001766		Approved		uc001frr.3	P15813	OTTHUMG00000022436	ENST00000368171.3:c.74delT	1.37:g.158151257delT	ENSP00000357153:p.Leu25fs						p.L25fs	NM_001766.3	NP_001757.1	P15813	CD1D_HUMAN			3	573	+	all_hematologic(112;0.0378)		25					D3DVD5|Q5W0J3|Q9UMM3|Q9Y5M4	Frame_Shift_Del	DEL	ENST00000368171.3	37	c.74delT	CCDS1173.1																																																																																				0.592	CD1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058340.1	NM_001766		7	2641						7	2641	---	---	---	---
SMG7	9887	broad.mit.edu	37	1	183515266	183515267	+	Frame_Shift_Ins	INS	-	-	A			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr1:183515266_183515267insA	ENST00000347615.2	+	17	2655_2656	c.2536_2537insA	c.(2536-2538)gaafs	p.E846fs	SMG7_ENST00000508461.1_Frame_Shift_Ins_p.E804fs|SMG7_ENST00000515829.2_Frame_Shift_Ins_p.E800fs|SMG7_ENST00000367537.3_Frame_Shift_Ins_p.E829fs|SMG7_ENST00000507469.1_Frame_Shift_Ins_p.E800fs|SMG7_ENST00000456731.2_Frame_Shift_Ins_p.E758fs	NM_173156.2	NP_775179.1	Q92540	SMG7_HUMAN	SMG7 nonsense mediated mRNA decay factor	846					gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	protein phosphatase 2A binding (GO:0051721)	p.?(1)		breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(16)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	46						GCAGCCTCTAGAAAAAAAAATG	0.45																																						ENST00000367537.3																			1	Unknown(1)	p.?(1)	skin(1)	breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(16)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	46						c.(2485-2487)aaafs		SMG7 nonsense mediated mRNA decay factor																																				SO:0001589	frameshift_variant	9887				mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of dephosphorylation	cytoplasm|intermediate filament cytoskeleton|nucleus	protein phosphatase 2A binding	g.chr1:183515266_183515267insA	D87437	CCDS1355.1, CCDS41445.1, CCDS41445.2, CCDS53444.1, CCDS53445.1	1q25	2013-07-02	2013-07-02	2006-02-16	ENSG00000116698	ENSG00000116698			16792	protein-coding gene	gene with protein product	"""EST1 telomerase component homolog C (S. cerevisiae)"""	610964	"""chromosome 1 open reading frame 16"", ""smg-7 homolog, nonsense mediated mRNA decay factor (C. elegans)"""	C1orf16		14636577, 15721257	Standard	NM_173156		Approved	KIAA0250, EST1C, SGA56M, SMG-7	uc001gqf.3	Q92540	OTTHUMG00000035221	ENST00000347615.2:c.2545dupA	1.37:g.183515275_183515275dupA	ENSP00000340766:p.Glu846fs					SMG7_ENST00000456731.2_Frame_Shift_Ins_p.K758fs|SMG7_ENST00000515829.2_Frame_Shift_Ins_p.K800fs|SMG7_ENST00000508461.1_Frame_Shift_Ins_p.K804fs|SMG7_ENST00000347615.2_Frame_Shift_Ins_p.K846fs|SMG7_ENST00000507469.1_Frame_Shift_Ins_p.K800fs	p.K829fs			Q92540	SMG7_HUMAN			18	2680_2681	+			846			Gln/Pro-rich.		B4DRB2|E9PCI0|E9PEH2|Q5T1Q0|Q6PIE0|Q7Z7H9|Q8IXC1|Q8IXC2	Frame_Shift_Ins	INS	ENST00000347615.2	37	c.2485_2486insA	CCDS1355.1																																																																																				0.450	SMG7-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000085432.1	NM_014837		17	425						17	425	---	---	---	---
APOBEC4	403314	broad.mit.edu	37	1	183616826	183616828	+	In_Frame_Del	DEL	TTC	TTC	-	rs141411396		TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr1:183616826_183616828delTTC	ENST00000308641.4	-	2	1360_1362	c.1089_1091delGAA	c.(1087-1092)aagaaa>aaa	p.363_364KK>K	RGL1_ENST00000304685.4_Intron|RGL1_ENST00000536277.1_Intron|APOBEC4_ENST00000481562.1_5'UTR	NM_203454.2	NP_982279.1	Q8WW27	ABEC4_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 4 (putative)	363					mRNA processing (GO:0006397)		hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines (GO:0016814)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(6)|skin(1)	21						TTTCTTCCCTTTCTTCTTCTTCT	0.419																																						ENST00000308641.4																			0				NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(6)|skin(1)	21						c.(1087-1092)aaa>aa		apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 4 (putative)																																				SO:0001651	inframe_deletion	403314				mRNA processing		hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines|zinc ion binding	g.chr1:183616826_183616828delTTC	BC021711	CCDS1358.1	1q25.3	2008-02-05	2005-10-27	2005-10-27	ENSG00000173627	ENSG00000173627		"""Apolipoprotein B mRNA editing enzymes"""	32152	protein-coding gene	gene with protein product		609908	"""chromosome 1 open reading frame 169"""	C1orf169		16082223	Standard	NM_203454		Approved	MGC26594, FLJ25691, RP1-127C7.4	uc001gqn.3	Q8WW27	OTTHUMG00000035459	ENST00000308641.4:c.1089_1091delGAA	1.37:g.183616835_183616837delTTC	ENSP00000310622:p.Lys364del					RGL1_ENST00000304685.3_Intron|RGL1_ENST00000367531.1_Intron|RGL1_ENST00000536277.1_Intron|APOBEC4_ENST00000481562.1_5'UTR	p.KK363del	NM_203454.2	NP_982279.1	Q8WW27	ABEC4_HUMAN			2	1360_1362	-			363					Q8N7F6	In_Frame_Del	DEL	ENST00000308641.4	37	c.1089_1091delGAA	CCDS1358.1																																																																																				0.419	APOBEC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086126.1	NM_203454		11	909						11	909	---	---	---	---
MTR	4548	broad.mit.edu	37	1	237024474	237024474	+	Frame_Shift_Del	DEL	A	A	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr1:237024474delA	ENST00000366577.5	+	20	2487	c.2093delA	c.(2092-2094)caafs	p.Q698fs	MTR_ENST00000535889.1_Intron	NM_000254.2	NP_000245.2	Q99707	METH_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase	698	B12-binding N-terminal. {ECO:0000255|PROSITE-ProRule:PRU00666}.				cellular nitrogen compound metabolic process (GO:0034641)|cobalamin metabolic process (GO:0009235)|methylation (GO:0032259)|nervous system development (GO:0007399)|pteridine-containing compound metabolic process (GO:0042558)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	cobalamin binding (GO:0031419)|methionine synthase activity (GO:0008705)|S-adenosylmethionine-homocysteine S-methyltransferase activity (GO:0008898)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(30)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	67	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;2.79e-22)|all_epithelial(177;4.84e-14)|Breast(1374;0.00123)|Prostate(94;0.0181)|Lung SC(1967;0.0262)|Acute lymphoblastic leukemia(190;0.117)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)	KIRC - Kidney renal clear cell carcinoma(1967;0.248)	Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)|Tetrahydrofolic acid(DB00116)	AGGTTAAACCAAAAAAAATAT	0.308																																						ENST00000366577.5																			0				breast(4)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(30)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	67						c.(2092-2094)cafs		5-methyltetrahydrofolate-homocysteine methyltransferase	Hydroxocobalamin(DB00200)|L-Methionine(DB00134)|Tetrahydrofolic acid(DB00116)			61,4205		23,15,2095	67.0	69.0	68.0			3.8	1.0	1		69	81,8173		35,11,4081	no	frameshift	MTR	NM_000254.2		58,26,6176	A1A1,A1R,RR		0.9813,1.4299,1.1342			237024474	142,12378	2203	4300	6503	SO:0001589	frameshift_variant	4548				nervous system development|xenobiotic metabolic process	cytosol	cobalamin binding|homocysteine S-methyltransferase activity|methionine synthase activity|protein binding|zinc ion binding	g.chr1:237024474delA	U73338	CCDS1614.1, CCDS73054.1	1q43	2011-05-12			ENSG00000116984	ENSG00000116984	2.1.1.13		7468	protein-coding gene	gene with protein product		156570				8968735	Standard	NM_000254		Approved	cblG	uc001hyi.4	Q99707	OTTHUMG00000040060	ENST00000366577.5:c.2093delA	1.37:g.237024474delA	ENSP00000355536:p.Gln698fs					MTR_ENST00000535889.1_Intron	p.Q698fs	NM_000254.2	NP_000245.2	Q99707	METH_HUMAN	OV - Ovarian serous cystadenocarcinoma(106;0.0106)	KIRC - Kidney renal clear cell carcinoma(1967;0.248)	20	2487	+	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;2.79e-22)|all_epithelial(177;4.84e-14)|Breast(1374;0.00123)|Prostate(94;0.0181)|Lung SC(1967;0.0262)|Acute lymphoblastic leukemia(190;0.117)	698			B12-binding N-terminal.		A1L4N8|A9Z1W4|B9EGF7|Q99713|Q99723	Frame_Shift_Del	DEL	ENST00000366577.5	37	c.2093delA	CCDS1614.1																																																																																				0.308	MTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096632.2	NM_000254		8	457						8	457	---	---	---	---
TAF1B	9014	broad.mit.edu	37	2	9989570	9989571	+	Frame_Shift_Ins	INS	-	-	A	rs528368939		TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr2:9989570_9989571insA	ENST00000263663.5	+	3	374_375	c.186_187insA	c.(187-189)aaafs	p.K63fs	TAF1B_ENST00000402170.1_3'UTR|TAF1B_ENST00000396242.3_5'UTR	NM_005680.2	NP_005671	Q53T94	TAF1B_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, B, 63kDa	63	B-reader.				gene expression (GO:0010467)|RNA polymerase I transcriptional preinitiation complex assembly at the promoter for the nuclear large rRNA transcript (GO:0001189)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|RNA polymerase I core factor complex (GO:0070860)	metal ion binding (GO:0046872)|RNA polymerase I CORE element sequence-specific DNA binding (GO:0001164)|RNA polymerase I CORE element sequence-specific DNA binding transcription factor recruiting transcription factor activity (GO:0001187)|sequence-specific DNA binding transcription factor activity (GO:0003700)|TBP-class protein binding (GO:0017025)	p.K63fs*1(1)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|lung(4)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	14	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					ACCGGGGGCTTAAAAAAAAAAA	0.337																																						ENST00000263663.5																			1	Insertion - Frameshift(1)	p.K63fs*1(1)	upper_aerodigestive_tract(1)	breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|lung(4)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	14						c.(184-189)ctaaaafs		TATA box binding protein (TBP)-associated factor, RNA polymerase I, B, 63kDa																																				SO:0001589	frameshift_variant	9014				termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	nucleoplasm	DNA binding|sequence-specific DNA binding transcription factor activity	g.chr2:9989570_9989571insA	L39061	CCDS33143.1	2p25	2008-06-02	2002-08-29		ENSG00000115750	ENSG00000115750			11533	protein-coding gene	gene with protein product		604904	"""TATA box binding protein (TBP)-associated factor, RNA polymerase I, B, 63kD"""			7801123	Standard	NM_005680		Approved	TAFI63, SL1, RAF1B, RAFI63	uc002qzz.3	Q53T94	OTTHUMG00000151673	ENST00000263663.5:c.197dupA	2.37:g.9989581_9989581dupA	ENSP00000263663:p.Lys63fs					TAF1B_ENST00000396242.3_5'UTR|TAF1B_ENST00000402170.1_3'UTR	p.LK62fs	NM_005680.2	NP_005671.2	Q53T94	TAF1B_HUMAN			3	374_375	+	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)		62					B4DI42|F8WD72|Q15574|Q8WVC3	Frame_Shift_Ins	INS	ENST00000263663.5	37	c.186_187insA	CCDS33143.1																																																																																				0.337	TAF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323426.2	NM_005680		7	32						7	32	---	---	---	---
DHX57	90957	broad.mit.edu	37	2	39095411	39095413	+	In_Frame_Del	DEL	CCA	CCA	-	rs199521315|rs372484063|rs199910361	byFrequency	TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr2:39095411_39095413delCCA	ENST00000295373.6	-	2	261_263	c.135_137delTGG	c.(133-138)ggtgga>gga	p.45_46GG>G	DHX57_ENST00000479345.2_5'Flank	NM_198963.1	NP_945314.1	Q6P158	DHX57_HUMAN	DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57	45	Gly-rich.						ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(20)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	62		all_hematologic(82;0.248)				Gccgccacctccaccaccaccac	0.532														22	0.00439297	0.0159	0.0014	5008	,	,		13864	0.0		0.0	False		,,,				2504	0.0				Melanoma(191;1090 2095 4375 23729 47341)	ENST00000295373.6																			0				NS(2)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(20)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	62						c.(133-138)gga>gg		DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57																																				SO:0001651	inframe_deletion	90957						ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding|zinc ion binding	g.chr2:39095411_39095413delCCA	AF070590	CCDS1800.1	2p22.3	2008-02-05			ENSG00000163214	ENSG00000163214		"""DEAH-boxes"""	20086	protein-coding gene	gene with protein product							Standard	NM_198963		Approved	DDX57	uc002rrf.3	Q6P158	OTTHUMG00000102103	ENST00000295373.6:c.135_137delTGG	2.37:g.39095420_39095422delCCA	ENSP00000295373:p.Gly49del						p.GG47del	NM_198963.1	NP_945314.1	Q6P158	DHX57_HUMAN			2	261_263	-		all_hematologic(82;0.248)	47			Gly-rich.		A2RRC7|Q53SI4|Q6P9G1|Q7Z6H3|Q8NG17|Q96M33	In_Frame_Del	DEL	ENST00000295373.6	37	c.135_137delTGG	CCDS1800.1																																																																																				0.532	DHX57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219940.2	NM_145646		7	598						7	598	---	---	---	---
OTX1	5013	broad.mit.edu	37	2	63283259	63283261	+	In_Frame_Del	DEL	CCA	CCA	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr2:63283259_63283261delCCA	ENST00000282549.2	+	5	1149_1151	c.873_875delCCA	c.(871-876)ggccac>ggc	p.H301del	OTX1_ENST00000366671.3_In_Frame_Del_p.H301del	NM_014562.3	NP_055377.1	P32242	OTX1_HUMAN	orthodenticle homeobox 1	301	His-rich.				anterior/posterior pattern specification (GO:0009952)|diencephalon morphogenesis (GO:0048852)|inner ear morphogenesis (GO:0042472)|metencephalon development (GO:0022037)|midbrain development (GO:0030901)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			endometrium(1)|kidney(2)|large_intestine(6)|lung(6)|pancreas(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	20	Lung NSC(7;0.121)|all_lung(7;0.211)					AGTCCTCAGGccaccaccaccac	0.64																																						ENST00000366671.3																			0				endometrium(1)|kidney(2)|large_intestine(6)|lung(6)|pancreas(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	20						c.(871-876)ggc>gg		orthodenticle homeobox 1																																				SO:0001651	inframe_deletion	5013					nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity	g.chr2:63283259_63283261delCCA		CCDS1873.1	2p15	2011-06-20	2007-02-15		ENSG00000115507	ENSG00000115507		"""Homeoboxes / PRD class"""	8521	protein-coding gene	gene with protein product		600036	"""orthodenticle (Drosophila) homolog 1"", ""orthodenticle homolog 1 (Drosophila)"""			7959790	Standard	NM_001199770		Approved		uc002scd.3	P32242	OTTHUMG00000129454	ENST00000282549.2:c.873_875delCCA	2.37:g.63283268_63283270delCCA	ENSP00000282549:p.His301del					OTX1_ENST00000282549.2_In_Frame_Del_p.GH291del	p.GH291del	NM_001199770.1	NP_001186699.1	P32242	OTX1_HUMAN			5	1149_1151	+	Lung NSC(7;0.121)|all_lung(7;0.211)		291			His-rich.		A6NHA2|B3KTJ4|Q53TG6	In_Frame_Del	DEL	ENST00000282549.2	37	c.873_875delCCA	CCDS1873.1																																																																																				0.640	OTX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251617.1			9	486						9	486	---	---	---	---
DYSF	8291	broad.mit.edu	37	2	71801420	71801422	+	In_Frame_Del	DEL	CCG	CCG	-	rs377079619		TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr2:71801420_71801422delCCG	ENST00000258104.3	+	30	3544_3546	c.3267_3269delCCG	c.(3265-3270)ttccgc>ttc	p.R1093del	DYSF_ENST00000410020.3_In_Frame_Del_p.R1111del|DYSF_ENST00000429174.2_In_Frame_Del_p.R1093del|DYSF_ENST00000409744.1_In_Frame_Del_p.R1080del|DYSF_ENST00000410041.1_In_Frame_Del_p.R1111del|DYSF_ENST00000409651.1_In_Frame_Del_p.R1125del|DYSF_ENST00000409582.3_In_Frame_Del_p.R1110del|DYSF_ENST00000409366.1_In_Frame_Del_p.R1094del|DYSF_ENST00000413539.2_In_Frame_Del_p.R1124del|DYSF_ENST00000409762.1_In_Frame_Del_p.R1110del|DYSF_ENST00000394120.2_In_Frame_Del_p.R1094del	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	1093	Arg-rich.				plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)			autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						CAGATGCCTTCCGCCGCCGCCGC	0.655																																						ENST00000258104.3																			0				autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						c.(3265-3270)ttc>tt		dysferlin																																				SO:0001651	inframe_deletion	8291					cytoplasmic vesicle membrane|integral to membrane|sarcolemma	calcium-dependent phospholipid binding	g.chr2:71801420_71801422delCCG	AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"""fer-1-like family member 1"""	603009	"""limb girdle muscular dystrophy 2B (autosomal recessive)"""	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.3267_3269delCCG	2.37:g.71801429_71801431delCCG	ENSP00000258104:p.Arg1093del					DYSF_ENST00000410020.3_In_Frame_Del_p.FR1107del|DYSF_ENST00000394120.2_In_Frame_Del_p.FR1090del|DYSF_ENST00000409744.1_In_Frame_Del_p.FR1076del|DYSF_ENST00000410041.1_In_Frame_Del_p.FR1107del|DYSF_ENST00000429174.2_In_Frame_Del_p.FR1089del|DYSF_ENST00000409582.3_In_Frame_Del_p.FR1106del|DYSF_ENST00000409762.1_In_Frame_Del_p.FR1106del|DYSF_ENST00000409366.1_In_Frame_Del_p.FR1090del|DYSF_ENST00000413539.2_In_Frame_Del_p.FR1120del|DYSF_ENST00000409651.1_In_Frame_Del_p.FR1121del	p.FR1089del	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN			30	3544_3546	+			1089			Arg-rich.		A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	In_Frame_Del	DEL	ENST00000258104.3	37	c.3267_3269delCCG	CCDS1918.1																																																																																				0.655	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494		7	988						7	988	---	---	---	---
WBP1	23559	broad.mit.edu	37	2	74687550	74687550	+	Frame_Shift_Del	DEL	T	T	-	rs8469	byFrequency	TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr2:74687550delT	ENST00000233615.2	+	4	826	c.552delT	c.(550-552)cctfs	p.P184fs	WBP1_ENST00000393972.3_Frame_Shift_Del_p.P218fs|WBP1_ENST00000494741.1_3'UTR|WBP1_ENST00000409737.1_Frame_Shift_Del_p.P181fs|MOGS_ENST00000462443.1_5'Flank	NM_012477.3	NP_036609.1	Q96G27	WBP1_HUMAN	WW domain binding protein 1	184							WW domain binding (GO:0050699)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|ovary(1)|urinary_tract(1)	8						GTGCCCCCCCTCATCAGGAGG	0.612																																						ENST00000393972.3																			0				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|ovary(1)|urinary_tract(1)	8						c.(652-654)ccfs		WW domain binding protein 1							52.0	70.0	64.0					2																	74687550		2203	4299	6502	SO:0001589	frameshift_variant	23559						WW domain binding	g.chr2:74687550delT	U79457	CCDS1943.1	2p12	2012-04-20			ENSG00000239779	ENSG00000239779			12737	protein-coding gene	gene with protein product		606961				7644498	Standard	NM_012477		Approved	WBP-1	uc002slj.2	Q96G27	OTTHUMG00000129958	ENST00000233615.2:c.552delT	2.37:g.74687550delT	ENSP00000233615:p.Pro184fs					WBP1_ENST00000233615.2_Frame_Shift_Del_p.P184fs|WBP1_ENST00000494741.1_3'UTR|WBP1_ENST00000409737.1_Frame_Shift_Del_p.P181fs	p.P218fs			Q96G27	WBP1_HUMAN			5	857	+			184					B2RE02|O95637	Frame_Shift_Del	DEL	ENST00000233615.2	37	c.654delT	CCDS1943.1																																																																																				0.612	WBP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252221.2	NM_012477		8	796						8	796	---	---	---	---
ERCC3	2071	broad.mit.edu	37	2	128028913	128028913	+	Splice_Site	DEL	T	T	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr2:128028913delT	ENST00000285398.2	-	12	2038	c.1944delA	c.(1942-1944)aaa>aa	p.K648fs	ERCC3_ENST00000493187.2_Splice_Site_p.K584fs	NM_000122.1	NP_000113.1	P19447	ERCC3_HUMAN	excision repair cross-complementation group 3	648	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				7-methylguanosine mRNA capping (GO:0006370)|apoptotic process (GO:0006915)|DNA repair (GO:0006281)|DNA topological change (GO:0006265)|gene expression (GO:0010467)|hair cell differentiation (GO:0035315)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA duplex unwinding (GO:0000717)|nucleotide-excision repair, DNA incision (GO:0033683)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|protein localization (GO:0008104)|regulation of mitotic cell cycle phase transition (GO:1901990)|response to hypoxia (GO:0001666)|response to oxidative stress (GO:0006979)|response to UV (GO:0009411)|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 initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)|viral process (GO:0016032)	holo TFIIH complex (GO:0005675)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5' DNA helicase activity (GO:0043138)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|damaged DNA binding (GO:0003684)|dATP binding (GO:0032564)|DNA binding (GO:0003677)|GTP binding (GO:0005525)|peptide binding (GO:0042277)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	31	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.073)		CCACTTTACCTTTTTTAGCTC	0.527			"""Mis, S"""			"""skin basal cell, skin squamous cell, melanoma"""		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																													ENST00000493187.2			yes	Rec		Xeroderma pigmentosum (B)	2	2q21	2071	"""Mis, S"""	"""excision repair cross-complementing rodent repair deficiency, complementation group 3 (xeroderma pigmentosum group B complementing)"""			E		"""skin basal cell, skin squamous cell, melanoma"""			0				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	31						c.e12+1	Nucleotide excision repair (NER)	excision repair cross-complementing rodent repair deficiency, complementation group 3							178.0	172.0	174.0					2																	128028913		2203	4300	6503	SO:0001630	splice_region_variant	2071	Xeroderma Pigmentosum	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	cell cycle checkpoint|DNA topological change|hair cell differentiation|induction of apoptosis|interspecies interaction between organisms|mRNA capping|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA duplex unwinding|nucleotide-excision repair, DNA incision|positive regulation of transcription from RNA polymerase II promoter|positive regulation of viral transcription|protein localization|response to oxidative stress|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase I promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	holo TFIIH complex	3'-5' DNA helicase activity|ATP binding|damaged DNA binding|protein C-terminus binding|protein N-terminus binding|transcription factor binding	g.chr2:128028913delT	M31899	CCDS2144.1	2q21	2014-09-17	2014-03-07		ENSG00000163161	ENSG00000163161		"""General transcription factors"", ""General transcription factor IIH complex subunits"""	3435	protein-coding gene	gene with protein product	"""xeroderma pigmentosum group B complementing"""	133510	"""excision repair cross-complementing rodent repair deficiency, complementation group 3"""			8202161	Standard	NM_000122		Approved	XPB, BTF2, RAD25, TFIIH, GTF2H	uc002toh.1	P19447	OTTHUMG00000131530	ENST00000285398.2:c.1945+1A>-	2.37:g.128028913delT						ERCC3_ENST00000285398.2_Splice_Site_p.K648_splice	p.K584_splice			P19447	ERCC3_HUMAN		BRCA - Breast invasive adenocarcinoma(221;0.073)	12	2215	-	Colorectal(110;0.1)		648			Helicase C-terminal.		Q53QM0	Splice_Site	DEL	ENST00000285398.2	37	c.1753_splice	CCDS2144.1																																																																																				0.527	ERCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331028.1	NM_000122	Frame_Shift_Del	7	1288						7	1288	---	---	---	---
HIBCH	26275	broad.mit.edu	37	2	191161629	191161629	+	Frame_Shift_Del	DEL	T	T	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr2:191161629delT	ENST00000359678.5	-	3	423	c.129delA	c.(127-129)aaafs	p.K43fs	HIBCH_ENST00000392332.3_Frame_Shift_Del_p.K43fs	NM_014362.3|NM_198047.2	NP_055177.2|NP_932164.1	Q6NVY1	HIBCH_HUMAN	3-hydroxyisobutyryl-CoA hydrolase	43					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|valine catabolic process (GO:0006574)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	3-hydroxyisobutyryl-CoA hydrolase activity (GO:0003860)			NS(1)|breast(2)|endometrium(1)|large_intestine(1)|lung(5)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(1)	13			OV - Ovarian serous cystadenocarcinoma(117;0.000586)|Epithelial(96;0.0286)|all cancers(119;0.0814)			CCGTGCAACCTTTTTTTTCCA	0.353																																						ENST00000392332.3																			0				NS(1)|breast(2)|endometrium(1)|large_intestine(1)|lung(5)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(1)	13						c.(127-129)aafs		3-hydroxyisobutyryl-CoA hydrolase							116.0	104.0	108.0					2																	191161629		2203	4300	6503	SO:0001589	frameshift_variant	26275				branched chain family amino acid catabolic process	mitochondrial matrix	3-hydroxyisobutyryl-CoA hydrolase activity|protein binding	g.chr2:191161629delT	U66669	CCDS2304.1, CCDS46475.1	2q32.3	2010-04-29	2010-04-29		ENSG00000198130	ENSG00000198130	3.1.2.4		4908	protein-coding gene	gene with protein product		610690	"""3-hydroxyisobutyryl-Coenzyme A hydrolase"""			8824301	Standard	NM_014362		Approved		uc002uru.3	Q6NVY1	OTTHUMG00000132673	ENST00000359678.5:c.129delA	2.37:g.191161629delT	ENSP00000352706:p.Lys43fs					HIBCH_ENST00000359678.5_Frame_Shift_Del_p.K43fs	p.K43fs			Q6NVY1	HIBCH_HUMAN	OV - Ovarian serous cystadenocarcinoma(117;0.000586)|Epithelial(96;0.0286)|all cancers(119;0.0814)		3	268	-			43					D3DPI4|Q53GA8|Q53GF2|Q53RF7|Q53TC6|Q92931|Q9BS94	Frame_Shift_Del	DEL	ENST00000359678.5	37	c.129delA	CCDS2304.1																																																																																				0.353	HIBCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255933.1			10	306						10	306	---	---	---	---
ANKRD44	91526	broad.mit.edu	37	2	197943383	197943384	+	Frame_Shift_Del	DEL	TG	TG	-	rs139294990		TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr2:197943383_197943384delTG	ENST00000409153.1	-	16	1875_1876	c.1693_1694delCA	c.(1693-1695)catfs	p.H565fs	ANKRD44_ENST00000337207.5_Intron|ANKRD44_ENST00000328737.2_Intron|ANKRD44_ENST00000539527.1_Frame_Shift_Del_p.H493fs|ANKRD44_ENST00000450567.1_Intron|ANKRD44_ENST00000282272.8_Intron			Q8N8A2	ANR44_HUMAN	ankyrin repeat domain 44	0										NS(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(20)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	45			OV - Ovarian serous cystadenocarcinoma(117;0.246)			ATTTGGGGTATGTGTGTGTGTG	0.411																																						ENST00000409153.1																			0				NS(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(20)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	45						c.(1693-1695)tfs		ankyrin repeat domain 44																																				SO:0001589	frameshift_variant	91526						protein binding	g.chr2:197943383_197943384delTG	AK097086	CCDS33355.1, CCDS33355.2, CCDS74619.1	2q33.1	2013-01-10			ENSG00000065413	ENSG00000065413		"""Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"", ""Ankyrin repeat domain containing"""	25259	protein-coding gene	gene with protein product	"""protein phosphatase 6 ankyrin repeat subunit B"""						Standard	NM_153697		Approved	PP6-ARS-B	uc021vuj.1	Q8N8A2	OTTHUMG00000154411	ENST00000409153.1:c.1693_1694delCA	2.37:g.197943393_197943394delTG	ENSP00000387141:p.His565fs					ANKRD44_ENST00000539527.1_Frame_Shift_Del_p.H493fs|ANKRD44_ENST00000328737.2_Intron|ANKRD44_ENST00000282272.8_Intron|ANKRD44_ENST00000450567.1_Intron|ANKRD44_ENST00000337207.5_Intron	p.H565fs			Q8N8A2	ANR44_HUMAN	OV - Ovarian serous cystadenocarcinoma(117;0.246)		16	1875_1876	-			811					Q53SL9|Q6P480|Q86VL5|Q8IZ72|Q9UFA4	Frame_Shift_Del	DEL	ENST00000409153.1	37	c.1693_1694delCA																																																																																					0.411	ANKRD44-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000335114.3	NM_153697		14	93						14	93	---	---	---	---
SGOL2	151246	broad.mit.edu	37	2	201437003	201437004	+	Frame_Shift_Ins	INS	-	-	T			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr2:201437003_201437004insT	ENST00000357799.4	+	7	2032_2033	c.1934_1935insT	c.(1933-1938)aattttfs	p.NF645fs		NM_001160033.1|NM_001160046.1|NM_152524.5	NP_001153505.1|NP_001153518.1|NP_689737.4	Q562F6	SGOL2_HUMAN	shugoshin-like 2 (S. pombe)	645					meiotic sister chromatid cohesion, centromeric (GO:0051754)|mitotic cell cycle (GO:0000278)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic cohesin complex (GO:0030892)|nucleus (GO:0005634)				NS(2)|breast(2)|cervix(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	46						AAAAAAGGTAATTTTTTTTTCA	0.337																																						ENST00000357799.4																			0				NS(2)|breast(2)|cervix(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	46						c.(1933-1935)attfs		shugoshin-like 2 (S. pombe)																																				SO:0001589	frameshift_variant	151246				cell division|mitotic prometaphase	condensed chromosome kinetochore|cytosol|mitotic cohesin complex	protein binding	g.chr2:201437003_201437004insT	AY094614	CCDS42796.1	2q33.2	2008-02-05			ENSG00000163535	ENSG00000163535			30812	protein-coding gene	gene with protein product		612425					Standard	NM_001160046		Approved	TRIPIN, FLJ25211	uc002uvw.2	Q562F6	OTTHUMG00000154535	ENST00000357799.4:c.1943dupT	2.37:g.201437012_201437012dupT	ENSP00000350447:p.Asn645fs						p.I645fs	NM_001160033.1|NM_001160046.1|NM_152524.5	NP_001153505.1|NP_001153518.1|NP_689737.4	Q562F6	SGOL2_HUMAN			7	2032_2033	+			645					Q53RR9|Q53T20|Q86XY4|Q8IWK2|Q8IZK1|Q8N1Q5|Q96LQ3	Frame_Shift_Ins	INS	ENST00000357799.4	37	c.1934_1935insT	CCDS42796.1																																																																																				0.337	SGOL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335834.1	NM_152524		8	734						8	734	---	---	---	---
GIGYF2	26058	broad.mit.edu	37	2	233712228	233712230	+	In_Frame_Del	DEL	CAG	CAG	-	rs62640389|rs10555297|rs398061180|rs527464858|rs58340018	byFrequency	TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr2:233712228_233712230delCAG	ENST00000409547.1	+	29	3942_3944	c.3631_3633delCAG	c.(3631-3633)cagdel	p.Q1216del	GIGYF2_ENST00000373566.3_In_Frame_Del_p.Q1238del|GIGYF2_ENST00000373563.4_In_Frame_Del_p.Q1216del|GIGYF2_ENST00000409451.3_In_Frame_Del_p.Q1237del|GIGYF2_ENST00000409196.3_In_Frame_Del_p.Q1210del|GIGYF2_ENST00000409480.1_In_Frame_Del_p.Q1238del	NM_015575.3	NP_056390.2	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2	1216	Gln-rich.				adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|feeding behavior (GO:0007631)|homeostasis of number of cells within a tissue (GO:0048873)|insulin-like growth factor receptor signaling pathway (GO:0048009)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|musculoskeletal movement (GO:0050881)|negative regulation of translation (GO:0017148)|neuromuscular process controlling balance (GO:0050885)|post-embryonic development (GO:0009791)|spinal cord motor neuron differentiation (GO:0021522)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)	p.Q1216delQ(2)|p.Q1237delQ(1)		NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(17)|lung(11)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	63		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)		gcagctgccacagcagcagcagc	0.547																																						ENST00000373566.3																			3	Deletion - In frame(3)	p.Q1216delQ(2)|p.Q1237delQ(1)	breast(2)|ovary(1)	NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(17)|lung(11)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	63						c.(3697-3699)del		GRB10 interacting GYF protein 2																																				SO:0001651	inframe_deletion	26058				cell death		protein binding	g.chr2:233712228_233712230delCAG	U80751	CCDS33401.1, CCDS46542.1, CCDS46543.1	2q37.1	2011-07-06	2008-02-11	2008-02-11	ENSG00000204120	ENSG00000204120		"""Trinucleotide (CAG) repeat containing"""	11960	protein-coding gene	gene with protein product	"""GYF domain containing 2"""	612003	"""PERQ amino acid rich, with GYF domain 2"", ""PERQ amino acid rich, with GYF domain 3"", ""trinucleotide repeat containing 15"", ""Parkinson disease (autosomal recessive, early onset) 11"""	PERQ2, PERQ3, TNRC15, PARK11		9225980, 9734811, 12771153, 18358451, 19279319	Standard	NM_015575		Approved	KIAA0642, GYF2	uc002vtk.4	Q6Y7W6	OTTHUMG00000153237	ENST00000409547.1:c.3631_3633delCAG	2.37:g.233712237_233712239delCAG	ENSP00000386537:p.Gln1216del					GIGYF2_ENST00000409480.1_In_Frame_Del_p.Q1238del|GIGYF2_ENST00000409547.1_In_Frame_Del_p.Q1216del|GIGYF2_ENST00000409451.3_In_Frame_Del_p.Q1237del|GIGYF2_ENST00000409196.3_In_Frame_Del_p.Q1210del|GIGYF2_ENST00000373563.4_In_Frame_Del_p.Q1216del	p.Q1238del			Q6Y7W6	PERQ2_HUMAN		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)	28	3894_3896	+		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)	1216			Gln-rich.		A6H8W4|B9EG55|E9PBB0|O75137|Q7Z2Z8|Q7Z3I2|Q96HU4|Q9NV82	In_Frame_Del	DEL	ENST00000409547.1	37	c.3697_3699delCAG	CCDS33401.1																																																																																				0.547	GIGYF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330316.2	NM_001103146		7	231						7	231	---	---	---	---
GAL3ST2	64090	broad.mit.edu	37	2	242738494	242738496	+	In_Frame_Del	DEL	TCC	TCC	-	rs199680376		TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr2:242738494_242738496delTCC	ENST00000192314.6	+	2	175_177	c.44_46delTCC	c.(43-48)atcctc>atc	p.L20del	AC114730.5_ENST00000437438.1_RNA	NM_022134.2	NP_071417.2	Q9H3Q3	G3ST2_HUMAN	galactose-3-O-sulfotransferase 2	20					biosynthetic process (GO:0009058)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	galactosylceramide sulfotransferase activity (GO:0001733)|sulfotransferase activity (GO:0008146)	p.L16I(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|prostate(1)|skin(1)	14		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;4.59e-33)|all cancers(36;9.89e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.89e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0833)		TTCCGGGTCATCCTCCTCCTCCT	0.631																																						ENST00000192314.6																			1	Substitution - Missense(1)	p.L16I(1)	prostate(1)	endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|prostate(1)|skin(1)	14						c.(43-48)atc>a		galactose-3-O-sulfotransferase 2																																				SO:0001651	inframe_deletion	64090				biosynthetic process	Golgi cisterna membrane|integral to membrane	galactosylceramide sulfotransferase activity	g.chr2:242738494_242738496delTCC	AB040610	CCDS33427.1	2q37.2	2014-05-19			ENSG00000154252	ENSG00000154252		"""Sulfotransferases, membrane-bound"""	24869	protein-coding gene	gene with protein product		608237				11029462	Standard	NM_022134		Approved	GP3ST	uc002wcj.1	Q9H3Q3	OTTHUMG00000151473	ENST00000192314.6:c.44_46delTCC	2.37:g.242738503_242738505delTCC	ENSP00000192314:p.Leu20del						p.IL15del	NM_022134.2	NP_071417.2	Q9H3Q3	G3ST2_HUMAN		Epithelial(32;4.59e-33)|all cancers(36;9.89e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.89e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0833)	2	175_177	+		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)	15					Q17RK0|Q57Z52	In_Frame_Del	DEL	ENST00000192314.6	37	c.44_46delTCC	CCDS33427.1																																																																																				0.631	GAL3ST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322792.1	NM_022134		8	423						8	423	---	---	---	---
EDEM1	9695	broad.mit.edu	37	3	5248941	5248941	+	Frame_Shift_Del	DEL	T	T	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr3:5248941delT	ENST00000256497.4	+	7	1454	c.1321delT	c.(1321-1323)tttfs	p.F442fs	EDEM1_ENST00000445686.1_Frame_Shift_Del_p.F247fs	NM_014674.2	NP_055489.1	Q92611	EDEM1_HUMAN	ER degradation enhancer, mannosidase alpha-like 1	442					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)	calcium ion binding (GO:0005509)|misfolded protein binding (GO:0051787)			NS(1)|breast(1)|endometrium(1)|large_intestine(5)|liver(2)|lung(4)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	22				Epithelial(13;0.0588)|OV - Ovarian serous cystadenocarcinoma(96;0.0682)		TCTGCAGGCCTTTTTCCCTGG	0.463																																						ENST00000256497.4																			0				NS(1)|breast(1)|endometrium(1)|large_intestine(5)|liver(2)|lung(4)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	22						c.(1321-1323)ttfs		ER degradation enhancer, mannosidase alpha-like 1							155.0	149.0	151.0					3																	5248941		2203	4300	6503	SO:0001589	frameshift_variant	9695				ER-associated protein catabolic process|post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine|response to unfolded protein	integral to endoplasmic reticulum membrane	calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity|misfolded protein binding	g.chr3:5248941delT	D86967	CCDS33686.1	3p26.1	2008-02-05			ENSG00000134109	ENSG00000134109			18967	protein-coding gene	gene with protein product		607673				12610306	Standard	NM_014674		Approved	KIAA0212, EDEM	uc003bqi.3	Q92611	OTTHUMG00000154896	ENST00000256497.4:c.1321delT	3.37:g.5248941delT	ENSP00000256497:p.Phe442fs					EDEM1_ENST00000445686.1_Frame_Shift_Del_p.F247fs	p.F442fs	NM_014674.2	NP_055489.1	Q92611	EDEM1_HUMAN		Epithelial(13;0.0588)|OV - Ovarian serous cystadenocarcinoma(96;0.0682)	7	1454	+			442					A8K9C8|B4DXP3	Frame_Shift_Del	DEL	ENST00000256497.4	37	c.1321delT	CCDS33686.1																																																																																				0.463	EDEM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337566.2	NM_014674		8	671						8	671	---	---	---	---
LNP1	348801	broad.mit.edu	37	3	100148586	100148588	+	In_Frame_Del	DEL	GAT	GAT	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr3:100148586_100148588delGAT	ENST00000383693.3	+	2	1293_1295	c.13_15delGAT	c.(13-15)gatdel	p.D10del	LNP1_ENST00000489752.1_In_Frame_Del_p.D10del	NM_001085451.1	NP_001078920.1	A1A4G5	LNP1_HUMAN	leukemia NUP98 fusion partner 1	10	Poly-Asp.									cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)	6						GGAGCACAAAGATGATGATGATG	0.507																																						ENST00000383693.3																			0				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)	6						c.(13-15)del		leukemia NUP98 fusion partner 1																																				SO:0001651	inframe_deletion	348801							g.chr3:100148586_100148588delGAT		CCDS43120.1	3q12.2	2014-05-12			ENSG00000206535	ENSG00000206535			28014	protein-coding gene	gene with protein product						16467868	Standard	NM_001085451		Approved	NP3	uc003dtx.4	A1A4G5	OTTHUMG00000159082	ENST00000383693.3:c.13_15delGAT	3.37:g.100148595_100148597delGAT	ENSP00000373191:p.Asp10del					LNP1_ENST00000489752.1_In_Frame_Del_p.D10del	p.D10del	NM_001085451.1	NP_001078920.1	A1A4G5	LNP1_HUMAN			2	1293_1295	+			10			Poly-Asp.		B7ZLT3	In_Frame_Del	DEL	ENST00000383693.3	37	c.13_15delGAT	CCDS43120.1																																																																																				0.507	LNP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353232.1			8	1362						8	1362	---	---	---	---
UROC1	131669	broad.mit.edu	37	3	126220106	126220106	+	Frame_Shift_Del	DEL	T	T	-	rs569784894		TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr3:126220106delT	ENST00000290868.2	-	10	973	c.920delA	c.(919-921)aagfs	p.K307fs	UROC1_ENST00000383579.3_Frame_Shift_Del_p.K367fs	NM_144639.2	NP_653240.1	Q96N76	HUTU_HUMAN	urocanate hydratase 1	307					cellular nitrogen compound metabolic process (GO:0034641)|histidine catabolic process (GO:0006548)|histidine catabolic process to glutamate and formamide (GO:0019556)|histidine catabolic process to glutamate and formate (GO:0019557)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	urocanate hydratase activity (GO:0016153)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(27)|ovary(1)|skin(1)	39				GBM - Glioblastoma multiforme(114;0.17)		GAGCACCTCCTTTTTTTTCCT	0.587																																						ENST00000290868.2																			0				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(27)|ovary(1)|skin(1)	39						c.(919-921)agfs		urocanate hydratase 1							209.0	200.0	203.0					3																	126220106		2203	4300	6503	SO:0001589	frameshift_variant	131669				histidine catabolic process	cytosol	urocanate hydratase activity	g.chr3:126220106delT	AK055862	CCDS3038.1, CCDS54636.1	3q21.2	2012-08-21	2012-08-21		ENSG00000159650	ENSG00000159650	4.2.1.49		26444	protein-coding gene	gene with protein product	"""urocanase 1"""	613012	"""urocanase domain containing 1"""			19304569	Standard	NM_144639		Approved	FLJ31300, HMFN0320	uc010hsi.2	Q96N76	OTTHUMG00000162753	ENST00000290868.2:c.920delA	3.37:g.126220106delT	ENSP00000290868:p.Lys307fs					UROC1_ENST00000383579.3_Frame_Shift_Del_p.K367fs	p.K307fs	NM_144639.2	NP_653240.1	Q96N76	HUTU_HUMAN		GBM - Glioblastoma multiforme(114;0.17)	10	973	-			307					E9PE13|Q14C64|Q68CJ7	Frame_Shift_Del	DEL	ENST00000290868.2	37	c.920delA	CCDS3038.1																																																																																				0.587	UROC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370325.2	NM_144639		8	1250						8	1250	---	---	---	---
MED12L	116931	broad.mit.edu	37	3	151148114	151148116	+	In_Frame_Del	DEL	CAG	CAG	-	rs147600909		TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr3:151148114_151148116delCAG	ENST00000474524.1	+	42	6369_6371	c.6331_6333delCAG	c.(6331-6333)cagdel	p.Q2115del	MED12L_ENST00000273432.4_In_Frame_Del_p.Q1779del	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	2115	Gln-rich.					mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)	p.Q2111E(1)		NS(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(27)|lung(50)|ovary(6)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	128			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			GCAGCAGACCCAGCAGCAGCAGC	0.527																																						ENST00000474524.1																			1	Substitution - Missense(1)	p.Q2111E(1)	lung(1)	NS(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(27)|lung(50)|ovary(6)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	128						c.(6331-6333)del		mediator complex subunit 12-like																																				SO:0001651	inframe_deletion	116931				regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex		g.chr3:151148114_151148116delCAG	AB046855, AF388364	CCDS33876.1	3q25.1	2007-07-30	2007-07-30		ENSG00000144893	ENSG00000144893			16050	protein-coding gene	gene with protein product		611318	"""mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)-like"""			11524702	Standard	XM_006713487		Approved	KIAA1635, TNRC11L, TRALPUSH, TRALP	uc003eyp.3	Q86YW9	OTTHUMG00000159844	ENST00000474524.1:c.6331_6333delCAG	3.37:g.151148123_151148125delCAG	ENSP00000417235:p.Gln2115del					MED12L_ENST00000273432.4_In_Frame_Del_p.Q1779del	p.Q2115del	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)		42	6369_6371	+			2115			Gln-rich.		Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	In_Frame_Del	DEL	ENST00000474524.1	37	c.6331_6333delCAG	CCDS33876.1																																																																																				0.527	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002		10	535						10	535	---	---	---	---
EIF4G1	1981	broad.mit.edu	37	3	184039744	184039746	+	In_Frame_Del	DEL	GAA	GAA	-	rs530167757	byFrequency	TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr3:184039744_184039746delGAA	ENST00000346169.2	+	10	1643_1645	c.1372_1374delGAA	c.(1372-1374)gaadel	p.E465del	EIF4G1_ENST00000319274.6_In_Frame_Del_p.E465del|EIF4G1_ENST00000350481.5_In_Frame_Del_p.E301del|EIF4G1_ENST00000414031.1_In_Frame_Del_p.E425del|EIF4G1_ENST00000352767.3_In_Frame_Del_p.E472del|EIF4G1_ENST00000411531.1_In_Frame_Del_p.E425del|EIF4G1_ENST00000424196.1_In_Frame_Del_p.E472del|EIF4G1_ENST00000441154.1_In_Frame_Del_p.E301del|EIF4G1_ENST00000434061.2_In_Frame_Del_p.E269del|EIF4G1_ENST00000427845.1_In_Frame_Del_p.E378del|EIF2B5_ENST00000444495.1_Intron|EIF4G1_ENST00000342981.4_In_Frame_Del_p.E465del|EIF4G1_ENST00000392537.2_In_Frame_Del_p.E378del|EIF4G1_ENST00000435046.2_In_Frame_Del_p.E269del|EIF4G1_ENST00000382330.3_In_Frame_Del_p.E472del	NM_198241.2	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4 gamma, 1	465	Poly-Glu.				cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|lung development (GO:0030324)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|response to ethanol (GO:0045471)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(5)|large_intestine(14)|lung(41)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	75	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			GGAGGAAATGgaagaagaagaag	0.562																																						ENST00000342981.4																			0				central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(5)|large_intestine(14)|lung(41)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	75						c.(1372-1374)del		eukaryotic translation initiation factor 4 gamma, 1																																				SO:0001651	inframe_deletion	1981				insulin receptor signaling pathway|interspecies interaction between organisms|nuclear-transcribed mRNA poly(A) tail shortening|regulation of translational initiation	cytosol|eukaryotic translation initiation factor 4F complex	protein binding|translation initiation factor activity	g.chr3:184039744_184039746delGAA	D12686	CCDS3259.1, CCDS3260.1, CCDS3261.1, CCDS46970.1, CCDS46970.2, CCDS54687.1, CCDS54688.1	3q27.1	2013-09-19			ENSG00000114867	ENSG00000114867		"""Parkinson disease"""	3296	protein-coding gene	gene with protein product		600495		EIF4G, EIF4F		1429670, 9372926, 21907011	Standard	NM_182917		Approved	p220, PARK18	uc010hxy.3	Q04637	OTTHUMG00000156784	ENST00000346169.2:c.1372_1374delGAA	3.37:g.184039753_184039755delGAA	ENSP00000316879:p.Glu465del					EIF4G1_ENST00000352767.3_In_Frame_Del_p.E472del|EIF4G1_ENST00000350481.5_In_Frame_Del_p.E301del|EIF4G1_ENST00000392537.2_In_Frame_Del_p.E378del|EIF4G1_ENST00000319274.6_In_Frame_Del_p.E465del|EIF4G1_ENST00000441154.1_In_Frame_Del_p.E301del|EIF4G1_ENST00000424196.1_In_Frame_Del_p.E472del|EIF4G1_ENST00000434061.2_In_Frame_Del_p.E269del|EIF4G1_ENST00000435046.2_In_Frame_Del_p.E269del|EIF4G1_ENST00000411531.1_In_Frame_Del_p.E425del|EIF2B5_ENST00000444495.1_Intron|EIF4G1_ENST00000346169.2_In_Frame_Del_p.E465del|EIF4G1_ENST00000427845.1_In_Frame_Del_p.E378del|EIF4G1_ENST00000414031.1_In_Frame_Del_p.E425del|EIF4G1_ENST00000382330.3_In_Frame_Del_p.E472del	p.E465del	NM_182917.4	NP_886553.3	Q04637	IF4G1_HUMAN	Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)		9	1786_1788	+	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		465			Poly-Glu.		D3DNT2|D3DNT4|D3DNT5|E9PFM1|G5E9S1|O43177|O95066|Q5HYG0|Q6ZN21|Q8N102	In_Frame_Del	DEL	ENST00000346169.2	37	c.1372_1374delGAA	CCDS3259.1																																																																																				0.562	EIF4G1-007	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000345733.1	NM_182917		12	606						12	606	---	---	---	---
ATP13A3	79572	broad.mit.edu	37	3	194181471	194181473	+	In_Frame_Del	DEL	GAG	GAG	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr3:194181471_194181473delGAG	ENST00000439040.1	-	4	930_932	c.139_141delCTC	c.(139-141)ctcdel	p.L47del	ATP13A3_ENST00000256031.4_In_Frame_Del_p.L47del			Q9H7F0	AT133_HUMAN	ATPase type 13A3	47						integral component of membrane (GO:0016021)|membrane (GO:0016020)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			NS(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	24	all_cancers(143;6.01e-09)|Ovarian(172;0.0634)	Melanoma(1037;0.211)	OV - Ovarian serous cystadenocarcinoma(49;3.83e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;5.98e-05)		GCATCCAATAGAGGAGGAGGAGG	0.463																																						ENST00000439040.1																			0				NS(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	24						c.(139-141)del		ATPase type 13A3																																				SO:0001651	inframe_deletion	79572				ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding	g.chr3:194181471_194181473delGAG	AJ306929	CCDS43187.1	3q29	2010-04-20			ENSG00000133657	ENSG00000133657		"""ATPases / P-type"""	24113	protein-coding gene	gene with protein product	"""ATPase family homolog up regulated in senescence cells"""	610232				11867234	Standard	NM_024524		Approved	AFURS1	uc003fty.4	Q9H7F0	OTTHUMG00000156034	ENST00000439040.1:c.139_141delCTC	3.37:g.194181480_194181482delGAG	ENSP00000416508:p.Leu47del					ATP13A3_ENST00000256031.4_In_Frame_Del_p.L47del	p.L47del			Q9H7F0	AT133_HUMAN	OV - Ovarian serous cystadenocarcinoma(49;3.83e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;5.98e-05)	4	930_932	-	all_cancers(143;6.01e-09)|Ovarian(172;0.0634)	Melanoma(1037;0.211)	47					Q8NC11|Q96KS1	In_Frame_Del	DEL	ENST00000439040.1	37	c.139_141delCTC	CCDS43187.1																																																																																				0.463	ATP13A3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342799.2	NM_024524		8	716						8	716	---	---	---	---
TMEM175	84286	broad.mit.edu	37	4	946206	946207	+	Frame_Shift_Del	DEL	TG	TG	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr4:946206_946207delTG	ENST00000264771.4	+	7	615_616	c.430_431delTG	c.(430-432)tgtfs	p.C144fs	TMEM175_ENST00000508204.1_Frame_Shift_Del_p.C62fs|TMEM175_ENST00000504180.1_3'UTR|TMEM175_ENST00000515740.1_Frame_Shift_Del_p.C28fs	NM_032326.2	NP_115702.1	Q9BSA9	TM175_HUMAN	transmembrane protein 175	144						integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)				NS(1)|endometrium(1)|large_intestine(2)|lung(6)|pancreas(1)|upper_aerodigestive_tract(3)	14			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			CTTCTTGTTCTGTGTGTGTGTG	0.515																																						ENST00000264771.4																			0				NS(1)|endometrium(1)|large_intestine(2)|lung(6)|pancreas(1)|upper_aerodigestive_tract(3)	14						c.(430-432)tfs		transmembrane protein 175																																				SO:0001589	frameshift_variant	84286					integral to membrane		g.chr4:946206_946207delTG	BC005158	CCDS3341.1, CCDS75087.1, CCDS75088.1	4p16.3	2008-02-05			ENSG00000127419	ENSG00000127419			28709	protein-coding gene	gene with protein product						12477932	Standard	XM_005272301		Approved	MGC4618	uc003gbq.3	Q9BSA9	OTTHUMG00000118996	ENST00000264771.4:c.430_431delTG	4.37:g.946216_946217delTG	ENSP00000264771:p.Cys144fs					TMEM175_ENST00000504180.1_3'UTR|TMEM175_ENST00000515740.1_Frame_Shift_Del_p.C28fs|TMEM175_ENST00000508204.1_Frame_Shift_Del_p.C62fs	p.C144fs	NM_032326.2	NP_115702.1	Q9BSA9	TM175_HUMAN	OV - Ovarian serous cystadenocarcinoma(23;0.0158)		7	615_616	+			144					D3DVN4|Q8ND13	Frame_Shift_Del	DEL	ENST00000264771.4	37	c.430_431delTG	CCDS3341.1																																																																																				0.515	TMEM175-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239193.2	NM_032326		8	1089						8	1089	---	---	---	---
CRIPAK	285464	broad.mit.edu	37	4	1389361	1389362	+	Frame_Shift_Del	DEL	CA	CA	-	rs571164794	byFrequency	TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr4:1389361_1389362delCA	ENST00000324803.4	+	1	4022_4023	c.1062_1063delCA	c.(1060-1065)ctcacafs	p.T355fs		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	355					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			CCCGCCTGCTCACACGTGCCCA	0.653														3	0.000599042	0.0015	0.0	5008	,	,		19095	0.0		0.001	False		,,,				2504	0.0					ENST00000324803.4																			0				NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35						c.(1060-1065)ctcafs		cysteine-rich PAK1 inhibitor				8,4244		0,8,2118						-1.1	0.0			160	7,8229		0,7,4111	no	frameshift	CRIPAK	NM_175918.3		0,15,6229	A1A1,A1R,RR		0.085,0.1881,0.1201				15,12473				SO:0001589	frameshift_variant	285464				ER-nucleus signaling pathway|negative regulation of protein kinase activity|regulation of cytoskeleton organization|response to estrogen stimulus	endoplasmic reticulum|nucleus|plasma membrane	protein binding	g.chr4:1389361_1389362delCA	AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"""cysteine-rich PAK1inhibitor"""			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.1062_1063delCA	4.37:g.1389363_1389364delCA	ENSP00000323978:p.Thr355fs						p.LT354fs	NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	OV - Ovarian serous cystadenocarcinoma(23;0.0106)		1	4022_4023	+			354					Q8NB03	Frame_Shift_Del	DEL	ENST00000324803.4	37	c.1062_1063delCA	CCDS3349.1																																																																																				0.653	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918		12	2382						12	2382	---	---	---	---
SLC34A2	10568	broad.mit.edu	37	4	25678148	25678150	+	In_Frame_Del	DEL	GCT	GCT	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr4:25678148_25678150delGCT	ENST00000382051.3	+	13	1900_1902	c.1850_1852delGCT	c.(1849-1854)cgctgc>cgc	p.C622del	SLC34A2_ENST00000504570.1_In_Frame_Del_p.C621del|SLC34A2_ENST00000503434.1_In_Frame_Del_p.C621del	NM_001177998.1|NM_006424.2	NP_001171469.1|NP_006415	O95436	NPT2B_HUMAN	solute carrier family 34 (type II sodium/phosphate contransporter), member 2	622	Cys-rich.				aging (GO:0007568)|cellular phosphate ion homeostasis (GO:0030643)|in utero embryonic development (GO:0001701)|ion transport (GO:0006811)|phosphate ion transmembrane transport (GO:0035435)|phosphate ion transport (GO:0006817)|response to estradiol (GO:0032355)|response to estrogen (GO:0043627)|response to fructose (GO:0009750)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	phosphate ion binding (GO:0042301)|sodium ion binding (GO:0031402)|sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|sodium:phosphate symporter activity (GO:0005436)		SLC34A2/ROS1(14)	breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(9)|lung(18)|ovary(1)|prostate(1)|skin(4)	41		Breast(46;0.0503)				TTCCAGATGCgctgctgctgctg	0.64			T	ROS1	NSCLC																																	ENST00000382051.3				Dom	yes		4	4p15.2	10568	T	"""solute carrier family 34 (sodium phosphate), member 2"""			E	ROS1		NSCLC	SLC34A2/ROS1(14)	0				breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(9)|lung(18)|ovary(1)|prostate(1)|skin(4)	41						c.(1849-1854)cgc>c		solute carrier family 34 (type II sodium/phosphate contransporter), member 2																																				SO:0001651	inframe_deletion	10568				cellular phosphate ion homeostasis	apical plasma membrane|brush border membrane|integral to plasma membrane	phosphate binding|sodium ion binding|sodium-dependent phosphate transmembrane transporter activity|sodium:phosphate symporter activity	g.chr4:25678148_25678150delGCT	AF111856	CCDS3435.1, CCDS54750.1	4p15.2	2013-07-17	2013-07-17		ENSG00000157765	ENSG00000157765		"""Solute carriers"""	11020	protein-coding gene	gene with protein product		604217	"""solute carrier family 34 (sodium phosphate), member 2"""			10329428, 10610722	Standard	NM_006424		Approved	NAPI-3B	uc003grr.3	O95436	OTTHUMG00000097757	ENST00000382051.3:c.1850_1852delGCT	4.37:g.25678157_25678159delGCT	ENSP00000371483:p.Cys622del					SLC34A2_ENST00000504570.1_In_Frame_Del_p.RC616del|SLC34A2_ENST00000503434.1_In_Frame_Del_p.RC616del	p.RC617del	NM_001177998.1|NM_006424.2	NP_001171469.1|NP_006415.2	O95436	NPT2B_HUMAN			13	1900_1902	+		Breast(46;0.0503)	617			Cys-rich.		A5PL17|Q8N2K2|Q8WYA9|Q9P0V7	In_Frame_Del	DEL	ENST00000382051.3	37	c.1850_1852delGCT	CCDS3435.1																																																																																				0.640	SLC34A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214990.1	NM_006424		7	373						7	373	---	---	---	---
UGDH	7358	broad.mit.edu	37	4	39515752	39515753	+	Frame_Shift_Ins	INS	-	-	A			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr4:39515752_39515753insA	ENST00000316423.6	-	3	556_557	c.214_215insT	c.(214-216)tctfs	p.S72fs	UGDH_ENST00000501493.2_Frame_Shift_Ins_p.S72fs|UGDH_ENST00000507089.1_5'UTR|UGDH_ENST00000515398.1_5'UTR|UGDH_ENST00000506179.1_Frame_Shift_Ins_p.S72fs	NM_001184701.1|NM_003359.3	NP_001171630.1|NP_003350.1	O60701	UGDH_HUMAN	UDP-glucose 6-dehydrogenase	72					cellular glucuronidation (GO:0052695)|gastrulation with mouth forming second (GO:0001702)|glycosaminoglycan biosynthetic process (GO:0006024)|small molecule metabolic process (GO:0044281)|UDP-glucose metabolic process (GO:0006011)|UDP-glucuronate biosynthetic process (GO:0006065)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	electron carrier activity (GO:0009055)|NAD binding (GO:0051287)|UDP-glucose 6-dehydrogenase activity (GO:0003979)	p.S72fs*18(1)		breast(1)|central_nervous_system(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(10)|ovary(3)|skin(1)|urinary_tract(2)	27						AATATTGGTAGAAAAAAAAAGA	0.297																																						ENST00000316423.6																			1	Deletion - Frameshift(1)	p.S72fs*18(1)	large_intestine(1)	breast(1)|central_nervous_system(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(10)|ovary(3)|skin(1)|urinary_tract(2)	27						c.(214-216)tacfs		UDP-glucose 6-dehydrogenase	NADH(DB00157)																																			SO:0001589	frameshift_variant	7358				glycosaminoglycan biosynthetic process|UDP-glucose metabolic process|UDP-glucuronate biosynthetic process|xenobiotic metabolic process	cytosol	electron carrier activity|NAD binding|UDP-glucose 6-dehydrogenase activity	g.chr4:39515752_39515753insA	AF061016	CCDS3455.1, CCDS54757.1, CCDS54758.1	4p14	2011-11-16	2010-04-28		ENSG00000109814	ENSG00000109814	1.1.1.22		12525	protein-coding gene	gene with protein product		603370	"""UDP-glucose dehydrogenase"""			9737970, 10575217	Standard	NM_003359		Approved		uc003guk.2	O60701	OTTHUMG00000099371	ENST00000316423.6:c.215dupT	4.37:g.39515761_39515761dupA	ENSP00000319501:p.Ser72fs					UGDH_ENST00000501493.2_Frame_Shift_Ins_p.Y72fs|UGDH_ENST00000515398.1_5'UTR|UGDH_ENST00000506179.1_Frame_Shift_Ins_p.Y72fs|UGDH_ENST00000507089.1_5'UTR	p.Y72fs	NM_001184701.1|NM_003359.3	NP_001171630.1|NP_003350.1	O60701	UGDH_HUMAN			3	556_557	-			72					B3KUU2|B4DN25|O60589	Frame_Shift_Ins	INS	ENST00000316423.6	37	c.214_215insT	CCDS3455.1																																																																																				0.297	UGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216818.3	NM_003359		8	392						8	392	---	---	---	---
LOC101927237	101927237	broad.mit.edu	37	4	68312324	68312325	+	lincRNA	INS	-	-	T	rs557800813	byFrequency	TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr4:68312324_68312325insT	ENST00000502400.1	-	0	34																											ATAACCCAGACTTTTTTTTTTC	0.302													|||unknown(HR)	143	0.0285543	0.0794	0.0072	5008	,	,		16073	0.0139		0.002	False		,,,				2504	0.0174					ENST00000502400.1																			0																																																			0							g.chr4:68312324_68312325insT																													4.37:g.68312334_68312334dupT														0	34	-									RNA	INS	ENST00000502400.1	37																																																																																						0.302	RP11-584P21.2-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000361926.2			7	155						7	155	---	---	---	---
PROL1	58503	broad.mit.edu	37	4	71275429	71275429	+	Frame_Shift_Del	DEL	T	T	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr4:71275429delT	ENST00000399575.2	+	3	558	c.384delT	c.(382-384)cctfs	p.P128fs	PROL1_ENST00000514338.1_3'UTR	NM_021225.4	NP_067048.4	Q99935	PROL1_HUMAN	proline rich, lacrimal 1	128	Pro-rich.				negative regulation of endopeptidase activity (GO:0010951)|regulation of sensory perception of pain (GO:0051930)|retina homeostasis (GO:0001895)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	endopeptidase inhibitor activity (GO:0004866)|peptidase inhibitor activity (GO:0030414)			endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)|skin(3)	15		all_hematologic(202;0.196)				CTCCTATTCCTTTTTTTCTTG	0.428																																						ENST00000399575.2																			0				endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)|skin(3)	15						c.(382-384)ccfs		proline rich, lacrimal 1							196.0	196.0	196.0					4																	71275429		1858	4105	5963	SO:0001589	frameshift_variant	58503				regulation of sensory perception of pain	extracellular region	endopeptidase inhibitor activity	g.chr4:71275429delT	S83198	CCDS43235.1	4q13.3	2011-10-28	2005-02-07		ENSG00000171199	ENSG00000171199			17279	protein-coding gene	gene with protein product		608936	"""proline rich 1"""			8670737	Standard	NM_021225		Approved	BPLP, PRL1, opiorphin	uc003hfi.3	Q99935	OTTHUMG00000160845	ENST00000399575.2:c.384delT	4.37:g.71275429delT	ENSP00000382485:p.Pro128fs					PROL1_ENST00000514338.1_3'UTR	p.P128fs	NM_021225.4	NP_067048.4	Q99935	PROL1_HUMAN			3	558	+		all_hematologic(202;0.196)	128			Pro-rich.		A8MZ07|P85047	Frame_Shift_Del	DEL	ENST00000399575.2	37	c.384delT	CCDS43235.1																																																																																				0.428	PROL1-001	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000362639.1	NM_021225		7	923						7	923	---	---	---	---
MOB1B	92597	broad.mit.edu	37	4	71844994	71844995	+	Frame_Shift_Ins	INS	-	-	T			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr4:71844994_71844995insT	ENST00000309395.2	+	5	760_761	c.559_560insT	c.(559-561)attfs	p.I187fs	MOB1B_ENST00000396051.2_Frame_Shift_Ins_p.I192fs|MOB1B_ENST00000511449.1_Intron	NM_001244766.1|NM_173468.3	NP_001231695.1|NP_775739.1	Q7L9L4	MOB1B_HUMAN	MOB kinase activator 1B	187					hippo signaling (GO:0035329)|positive regulation of phosphorylation (GO:0042327)|protein autophosphorylation (GO:0046777)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	kinase activator activity (GO:0019209)|kinase binding (GO:0019900)|metal ion binding (GO:0046872)										CAAGCACTTTATTTTTTTTGTC	0.396																																						ENST00000309395.2																			0											c.(559-561)tttfs		MOB kinase activator 1B																																				SO:0001589	frameshift_variant	92597				hippo signaling cascade|protein autophosphorylation	cytoplasm|nucleus	kinase activator activity|kinase binding|metal ion binding	g.chr4:71844994_71844995insT	BC038112	CCDS34002.1, CCDS58903.1	4q13.3	2011-09-28	2011-09-28	2011-09-27	ENSG00000173542	ENSG00000173542		"""MOB kinase activators"""	29801	protein-coding gene	gene with protein product	"""Mob4A protein"""	609282	"""MOB1, Mps One Binder kinase activator-like 1A (yeast)"", ""MOB1 Mps One Binder homolog B (yeast)"""	MOBKL1A		15067004	Standard	NM_173468		Approved	MOB4A	uc003hfw.3	Q7L9L4	OTTHUMG00000160844	ENST00000309395.2:c.567dupT	4.37:g.71845002_71845002dupT	ENSP00000310189:p.Ile187fs					MOB1B_ENST00000396051.2_Frame_Shift_Ins_p.F192fs|MOB1B_ENST00000511449.1_Intron	p.F187fs	NM_001244766.1|NM_173468.3	NP_001231695.1|NP_775739.1	Q7L9L4	MOL1A_HUMAN			5	760_761	+			187					B2R8U6|B4DRY3|Q8IY23	Frame_Shift_Ins	INS	ENST00000309395.2	37	c.559_560insT	CCDS34002.1																																																																																				0.396	MOB1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362634.1	NM_173468		7	586						7	586	---	---	---	---
PTPN13	5783	broad.mit.edu	37	4	87622606	87622607	+	Frame_Shift_Ins	INS	-	-	A			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr4:87622606_87622607insA	ENST00000411767.2	+	7	910_911	c.847_848insA	c.(847-849)gaafs	p.E283fs	PTPN13_ENST00000436978.1_Frame_Shift_Ins_p.E283fs|PTPN13_ENST00000511467.1_Frame_Shift_Ins_p.E283fs|PTPN13_ENST00000316707.6_Frame_Shift_Ins_p.E283fs|PTPN13_ENST00000427191.2_Frame_Shift_Ins_p.E283fs			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	283					peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)			NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		TAGTGGCCCAGAAAAAAAACCC	0.401																																						ENST00000436978.1																			0				NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93						c.(847-849)aaafs		protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)			,,,	8,3532		3,2,1765					,,,	5.1	0.9			50	5,7821		1,3,3909	no	frameshift,frameshift,frameshift,frameshift	PTPN13	NM_080685.2,NM_080684.2,NM_080683.2,NM_006264.2	,,,	4,5,5674	A1A1,A1R,RR		0.0639,0.226,0.1144	,,,	,,,		13,11353				SO:0001589	frameshift_variant	0					cytoplasm|cytoskeleton|plasma membrane	protein binding|protein tyrosine phosphatase activity	g.chr4:87622606_87622607insA		CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.855dupA	4.37:g.87622614_87622614dupA	ENSP00000407249:p.Glu283fs					PTPN13_ENST00000511467.1_Frame_Shift_Ins_p.K283fs|PTPN13_ENST00000316707.6_Frame_Shift_Ins_p.K283fs|PTPN13_ENST00000411767.2_Frame_Shift_Ins_p.K283fs|PTPN13_ENST00000427191.2_Frame_Shift_Ins_p.K283fs	p.K283fs	NM_080683.2|NM_080685.2	NP_542414.1|NP_542416.1	Q12923	PTN13_HUMAN		OV - Ovarian serous cystadenocarcinoma(123;0.00082)	7	1327_1328	+		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)	283					B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Frame_Shift_Ins	INS	ENST00000411767.2	37	c.847_848insA	CCDS47094.1																																																																																				0.401	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1			7	223						7	223	---	---	---	---
MAML3	55534	broad.mit.edu	37	4	140810639	140810641	+	In_Frame_Del	DEL	GCT	GCT	-	rs372496848		TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr4:140810639_140810641delGCT	ENST00000509479.2	-	2	2805_2807	c.1949_1951delAGC	c.(1948-1953)cagccg>ccg	p.Q650del	MAML3_ENST00000327122.5_In_Frame_Del_p.Q494del|MAML3_ENST00000398940.1_In_Frame_Del_p.Q178del	NM_018717.4	NP_061187			mastermind-like 3 (Drosophila)											breast(1)|endometrium(7)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|urinary_tract(2)	25	all_hematologic(180;0.162)					GGAGGTGGCGgctgctgctgctg	0.586																																						ENST00000509479.2																			0				breast(1)|endometrium(7)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|urinary_tract(2)	25						c.(1948-1953)ccg>c		mastermind-like 3 (Drosophila)																																				SO:0001651	inframe_deletion	55534				Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear speck	transcription coactivator activity	g.chr4:140810639_140810641delGCT	AB058719	CCDS54805.1	4q31.1	2014-08-12	2003-09-24		ENSG00000196782	ENSG00000196782			16272	protein-coding gene	gene with protein product	"""mastermind (drosophila)-like 3"""	608991	"""trinucleotide repeat containing 3"""	TNRC3		12370315, 12386158	Standard	NM_018717		Approved	KIAA1816, MAM2, CAGH3, GDN	uc021xsg.1	Q96JK9	OTTHUMG00000161441	ENST00000509479.2:c.1949_1951delAGC	4.37:g.140810648_140810650delGCT	ENSP00000421180:p.Gln650del					MAML3_ENST00000327122.5_In_Frame_Del_p.QP494del|MAML3_ENST00000398940.1_In_Frame_Del_p.QP178del	p.QP650del	NM_018717.4	NP_061187.2	Q96JK9	MAML3_HUMAN			2	2805_2807	-	all_hematologic(180;0.162)		646			Gln-rich.			In_Frame_Del	DEL	ENST00000509479.2	37	c.1949_1951delAGC	CCDS54805.1																																																																																				0.586	MAML3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364934.2			17	435						17	435	---	---	---	---
MAML3	55534	broad.mit.edu	37	4	140811064	140811069	+	In_Frame_Del	DEL	TGCTGC	TGCTGC	-	rs58015886|rs370122702		TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr4:140811064_140811069delTGCTGC	ENST00000509479.2	-	2	2377_2382	c.1521_1526delGCAGCA	c.(1519-1527)cagcagcaa>caa	p.507_509QQQ>Q	MAML3_ENST00000327122.5_In_Frame_Del_p.351_353QQQ>Q|MAML3_ENST00000398940.1_Splice_Site_p.A37del	NM_018717.4	NP_061187			mastermind-like 3 (Drosophila)											breast(1)|endometrium(7)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|urinary_tract(2)	25	all_hematologic(180;0.162)					TGAGtgctgttgctgctgctgctgct	0.515																																						ENST00000509479.2																			0				breast(1)|endometrium(7)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|urinary_tract(2)	25						c.(1519-1527)caa>ca		mastermind-like 3 (Drosophila)																																				SO:0001651	inframe_deletion	55534				Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear speck	transcription coactivator activity	g.chr4:140811064_140811069delTGCTGC	AB058719	CCDS54805.1	4q31.1	2014-08-12	2003-09-24		ENSG00000196782	ENSG00000196782			16272	protein-coding gene	gene with protein product	"""mastermind (drosophila)-like 3"""	608991	"""trinucleotide repeat containing 3"""	TNRC3		12370315, 12386158	Standard	NM_018717		Approved	KIAA1816, MAM2, CAGH3, GDN	uc021xsg.1	Q96JK9	OTTHUMG00000161441	ENST00000509479.2:c.1521_1526delGCAGCA	4.37:g.140811070_140811075delTGCTGC	ENSP00000421180:p.Gln509_Gln510del					MAML3_ENST00000327122.5_In_Frame_Del_p.QQQ351del|MAML3_ENST00000398940.1_Splice_Site_p.37_splice	p.QQQ507del	NM_018717.4	NP_061187.2	Q96JK9	MAML3_HUMAN			2	2377_2382	-	all_hematologic(180;0.162)		506			Gln-rich.			In_Frame_Del	DEL	ENST00000509479.2	37	c.1521_1526delGCAGCA	CCDS54805.1																																																																																				0.515	MAML3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364934.2			39	557						39	557	---	---	---	---
DDX60	55601	broad.mit.edu	37	4	169182016	169182016	+	Splice_Site	DEL	A	A	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr4:169182016delA	ENST00000393743.3	-	25	3689	c.3398delT	c.(3397-3399)tta>ta	p.L1133fs	DDX60_ENST00000505393.1_5'UTR	NM_017631.5	NP_060101.3	Q8IY21	DDX60_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	1133					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|positive regulation of MDA-5 signaling pathway (GO:1900245)|positive regulation of RIG-I signaling pathway (GO:1900246)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)	ATP binding (GO:0005524)|double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|single-stranded RNA binding (GO:0003727)			breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(15)|liver(1)|lung(21)|ovary(1)|pancreas(2)|prostate(1)|skin(4)|urinary_tract(4)	63		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.0485)		AATAACTTACAAAAAAAATAG	0.383																																						ENST00000393743.3																			0				breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(15)|liver(1)|lung(21)|ovary(1)|pancreas(2)|prostate(1)|skin(4)|urinary_tract(4)	63						c.e25+1		DEAD (Asp-Glu-Ala-Asp) box polypeptide 60							55.0	62.0	60.0					4																	169182016		2201	4300	6501	SO:0001630	splice_region_variant	55601						ATP binding|ATP-dependent helicase activity|RNA binding	g.chr4:169182016delA	AK001649	CCDS34097.1	4q32.3	2010-02-17			ENSG00000137628	ENSG00000137628			25942	protein-coding gene	gene with protein product		613974				12477932	Standard	NM_017631		Approved	FLJ20035	uc003irp.3	Q8IY21	OTTHUMG00000161350	ENST00000393743.3:c.3398+1T>-	4.37:g.169182016delA						DDX60_ENST00000505393.1_5'UTR	p.L1133_splice	NM_017631.5	NP_060101.3	Q8IY21	DDX60_HUMAN		GBM - Glioblastoma multiforme(119;0.0485)	25	3689	-		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)	1133					Q6PK35|Q9NVE3	Splice_Site	DEL	ENST00000393743.3	37	c.3398_splice	CCDS34097.1																																																																																				0.383	DDX60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364622.1	NM_017631	Frame_Shift_Del	7	486						7	486	---	---	---	---
HMGB2	3148	broad.mit.edu	37	4	174253277	174253279	+	In_Frame_Del	DEL	TCC	TCC	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr4:174253277_174253279delTCC	ENST00000296503.5	-	5	1455_1457	c.582_584delGGA	c.(580-585)gaggaa>gaa	p.194_195EE>E	HMGB2_ENST00000438704.2_In_Frame_Del_p.194_195EE>E|RP11-798M19.3_ENST00000507803.1_RNA|HMGB2_ENST00000446922.2_In_Frame_Del_p.194_195EE>E			P26583	HMGB2_HUMAN	high mobility group box 2	194	Asp/Glu-rich (acidic).				apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|base-excision repair, DNA ligation (GO:0006288)|cell chemotaxis (GO:0060326)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to lipopolysaccharide (GO:0071222)|chromatin organization (GO:0006325)|DNA ligation involved in DNA repair (GO:0051103)|DNA topological change (GO:0006265)|male gonad development (GO:0008584)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive chemotaxis (GO:0050918)|positive regulation of DNA binding (GO:0043388)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of nuclease activity (GO:0032075)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to steroid hormone (GO:0048545)|spermatid nucleus differentiation (GO:0007289)|V(D)J recombination (GO:0033151)	condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)	chemoattractant activity (GO:0042056)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|RAGE receptor binding (GO:0050786)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription regulatory region DNA binding (GO:0044212)	p.E194E(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|urinary_tract(3)	14		Prostate(90;0.0132)|Renal(120;0.0183)|Melanoma(52;0.0749)|all_hematologic(60;0.107)|all_neural(102;0.122)		all cancers(43;9.58e-18)|Epithelial(43;3.75e-16)|OV - Ovarian serous cystadenocarcinoma(60;6.24e-09)|STAD - Stomach adenocarcinoma(60;0.00273)|GBM - Glioblastoma multiforme(59;0.0064)|LUSC - Lung squamous cell carcinoma(193;0.0903)|Kidney(143;0.249)		atcttcttcttcctcctcctcct	0.468																																						ENST00000296503.5																			1	Substitution - coding silent(1)	p.E194E(1)	endometrium(1)	endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|urinary_tract(3)	14						c.(580-585)gaa>ga		high mobility group box 2			,,	25,4237		10,5,2116					,,	-1.4	1.0			279	85,8161		40,5,4078	no	coding,coding,coding	HMGB2	NM_002129.3,NM_001130689.1,NM_001130688.1	,,	50,10,6194	A1A1,A1R,RR		1.0308,0.5866,0.8794	,,	,,		110,12398				SO:0001651	inframe_deletion	3148				base-excision repair, DNA ligation|cell chemotaxis|cellular response to lipopolysaccharide|DNA fragmentation involved in apoptotic nuclear change|DNA topological change|negative regulation of transcription, DNA-dependent|nucleosome assembly|phosphatidylinositol-mediated signaling|positive regulation of DNA binding|positive regulation of endothelial cell proliferation|positive regulation of erythrocyte differentiation|positive regulation of megakaryocyte differentiation|positive regulation of nuclease activity|positive regulation of transcription from RNA polymerase II promoter|V(D)J recombination	condensed chromosome|extracellular space|nucleolus|nucleoplasm|perinuclear region of cytoplasm|protein complex	chemoattractant activity|damaged DNA binding|DNA bending activity|double-stranded DNA binding|RAGE receptor binding|sequence-specific DNA binding transcription factor activity|single-stranded DNA binding|transcription regulatory region DNA binding	g.chr4:174253277_174253279delTCC		CCDS3816.1	4q31	2011-07-01	2011-04-05	2002-08-16	ENSG00000164104	ENSG00000164104		"""High-mobility group / Canonical"""	5000	protein-coding gene	gene with protein product		163906	"""high-mobility group (nonhistone chromosomal) protein 2"", ""high-mobility group box 2"""	HMG2		1754403	Standard	NM_002129		Approved		uc011ckc.1	P26583	OTTHUMG00000160799	ENST00000296503.5:c.582_584delGGA	4.37:g.174253286_174253288delTCC	ENSP00000296503:p.Glu197del					HMGB2_ENST00000438704.2_In_Frame_Del_p.EE196del|HMGB2_ENST00000446922.2_In_Frame_Del_p.EE196del	p.EE196del			P26583	HMGB2_HUMAN		all cancers(43;9.58e-18)|Epithelial(43;3.75e-16)|OV - Ovarian serous cystadenocarcinoma(60;6.24e-09)|STAD - Stomach adenocarcinoma(60;0.00273)|GBM - Glioblastoma multiforme(59;0.0064)|LUSC - Lung squamous cell carcinoma(193;0.0903)|Kidney(143;0.249)	5	1455_1457	-		Prostate(90;0.0132)|Renal(120;0.0183)|Melanoma(52;0.0749)|all_hematologic(60;0.107)|all_neural(102;0.122)	196			Asp/Glu-rich (acidic).		B2R4K8|D3DP37|Q5U072	In_Frame_Del	DEL	ENST00000296503.5	37	c.582_584delGGA	CCDS3816.1																																																																																				0.468	HMGB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362362.1	NM_001130688		8	530						8	530	---	---	---	---
CEP72	55722	broad.mit.edu	37	5	640649	640651	+	In_Frame_Del	DEL	AGC	AGC	-	rs141221365		TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr5:640649_640651delAGC	ENST00000264935.5	+	9	1559_1561	c.1469_1471delAGC	c.(1468-1473)gagcag>gag	p.Q494del	CEP72_ENST00000444221.1_3'UTR	NM_018140.3	NP_060610.2	Q9P209	CEP72_HUMAN	centrosomal protein 72kDa	494					G2/M transition of mitotic cell cycle (GO:0000086)|gamma-tubulin complex localization (GO:0033566)|mitotic cell cycle (GO:0000278)|spindle organization (GO:0007051)	centrosome (GO:0005813)|cytosol (GO:0005829)				autonomic_ganglia(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(1)|liver(1)|lung(5)|ovary(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(2)	20			Epithelial(17;0.000339)|all cancers(22;0.00137)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|Lung(60;0.0863)			CGCCTTGCTGAGCAGCAGCAGCA	0.621																																						ENST00000264935.5																			0				autonomic_ganglia(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(1)|liver(1)|lung(5)|ovary(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(2)	20						c.(1468-1473)gag>g		centrosomal protein 72kDa				126,4140		62,2,2069						4.2	0.1		dbSNP_134	76	220,8034		107,6,4014	no	coding	CEP72	NM_018140.3		169,8,6083	A1A1,A1R,RR		2.6654,2.9536,2.7636				346,12174				SO:0001651	inframe_deletion	55722				G2/M transition of mitotic cell cycle|gamma-tubulin complex localization|spindle organization	centrosome|cytosol		g.chr5:640649_640651delAGC	BC000132	CCDS34126.1	5p15.33	2014-02-20			ENSG00000112877	ENSG00000112877			25547	protein-coding gene	gene with protein product						10819331	Standard	NM_018140		Approved	KIAA1519, FLJ10565	uc003jbf.3	Q9P209	OTTHUMG00000161745	ENST00000264935.5:c.1469_1471delAGC	5.37:g.640658_640660delAGC	ENSP00000264935:p.Gln494del					CEP72_ENST00000444221.1_3'UTR	p.EQ490del	NM_018140.3	NP_060610.2	Q9P209	CEP72_HUMAN	Epithelial(17;0.000339)|all cancers(22;0.00137)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|Lung(60;0.0863)		9	1559_1561	+			490					B4DR26|Q9BV03|Q9BWM3|Q9NVR4	In_Frame_Del	DEL	ENST00000264935.5	37	c.1469_1471delAGC	CCDS34126.1																																																																																				0.621	CEP72-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000365967.3	NM_018140		7	304						7	304	---	---	---	---
NPR3	4883	broad.mit.edu	37	5	32789822	32789823	+	3'UTR	DEL	GT	GT	-	rs370388563		TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr5:32789822_32789823delGT	ENST00000265074.8	+	0	5340_5341				AC026703.1_ENST00000326958.1_Frame_Shift_Del_p.C106fs	NM_000908.3|NM_001204375.1	NP_000899.1|NP_001191304.1	P17342	ANPRC_HUMAN	natriuretic peptide receptor 3						adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of smooth muscle cell proliferation (GO:0048662)|osteoclast proliferation (GO:0002158)|pancreatic juice secretion (GO:0030157)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of urine volume (GO:0035810)|regulation of blood pressure (GO:0008217)|regulation of osteoblast proliferation (GO:0033688)|skeletal system development (GO:0001501)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	G-protein coupled peptide receptor activity (GO:0008528)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	24					Nesiritide(DB04899)	CTGATTTTGGGTGTGTGTGTGT	0.421																																						ENST00000326958.1																			0											c.(313-318)gggtfs																																						SO:0001624	3_prime_UTR_variant	0							g.chr5:32789822_32789823delGT		CCDS47196.1, CCDS56356.1, CCDS56357.1	5p13.3	2014-03-03	2014-03-03		ENSG00000113389	ENSG00000113389			7945	protein-coding gene	gene with protein product	"""guanylate cyclase C"""	108962	"""chromosome 5 open reading frame 23"", ""atrionatriuretic peptide receptor C"", ""natriuretic peptide receptor C/guanylate cyclase C (atrionatriuretic peptide receptor C)"", ""natriuretic peptide receptor C"""	NPRC, ANPRC, C5orf23		2162522, 1979052	Standard	NM_000908		Approved	GUCY2B, FLJ14054	uc003jhv.3	P17342	OTTHUMG00000150316	ENST00000265074.8:c.*3372GT>-	5.37:g.32789832_32789833delGT						NPR3_ENST00000265074.8_3'UTR	p.GC105fs							1	878_879	+								A2RRD1|B4DT84|E7EPG9	Frame_Shift_Del	DEL	ENST00000265074.8	37	c.315_316delGT	CCDS56357.1																																																																																				0.421	NPR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317550.3	NM_000908		7	482						7	482	---	---	---	---
EGR1	1958	broad.mit.edu	37	5	137801633	137801635	+	In_Frame_Del	DEL	CAG	CAG	-	rs555024246|rs140268489		TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr5:137801633_137801635delCAG	ENST00000239938.4	+	1	455_457	c.183_185delCAG	c.(181-186)aacagc>aac	p.S67del		NM_001964.2	NP_001955.1	P18146	EGR1_HUMAN	early growth response 1	67	Gly/Ser-rich.				BMP signaling pathway (GO:0030509)|cellular response to antibiotic (GO:0071236)|cellular response to cAMP (GO:0071320)|cellular response to drug (GO:0035690)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to gamma radiation (GO:0071480)|cellular response to gonadotropin stimulus (GO:0071371)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heparin (GO:0071504)|cellular response to hyperoxia (GO:0071455)|cellular response to hypoxia (GO:0071456)|cellular response to insulin stimulus (GO:0032869)|cellular response to isoquinoline alkaloid (GO:0071317)|cellular response to mechanical stimulus (GO:0071260)|cellular response to mycophenolic acid (GO:0071506)|cellular response to steroid hormone stimulus (GO:0071383)|circadian rhythm (GO:0007623)|cytokine-mediated signaling pathway (GO:0019221)|glomerular mesangial cell proliferation (GO:0072110)|interleukin-1-mediated signaling pathway (GO:0070498)|learning or memory (GO:0007611)|long-term synaptic potentiation (GO:0060291)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oligodendrocyte differentiation (GO:0048709)|positive regulation of glomerular metanephric mesangial cell proliferation (GO:0072303)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of protein sumoylation (GO:0033233)|response to amphetamine (GO:0001975)|response to carbon monoxide (GO:0034465)|response to cocaine (GO:0042220)|response to electrical stimulus (GO:0051602)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to norepinephrine (GO:0071873)|response to nutrient levels (GO:0031667)|skeletal muscle cell differentiation (GO:0035914)|T cell differentiation (GO:0030217)|transcription from RNA polymerase II promoter (GO:0006366)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|histone acetyltransferase binding (GO:0035035)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|ovary(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)			gcggcagcaacagcagcagcagc	0.7																																						ENST00000239938.4																			0				haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|ovary(1)	6						c.(181-186)aac>aa		early growth response 1																																				SO:0001651	inframe_deletion	1958				cellular response to heparin|cellular response to mycophenolic acid|glomerular mesangial cell proliferation|interleukin-1-mediated signaling pathway|positive regulation of glomerular metanephric mesangial cell proliferation|positive regulation of transcription from RNA polymerase II promoter|regulation of protein sumoylation|transcription from RNA polymerase II promoter|type I interferon-mediated signaling pathway	cytoplasm|nucleus	histone acetyltransferase binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding	g.chr5:137801633_137801635delCAG	M62829	CCDS4206.1	5q23-q31	2013-01-08			ENSG00000120738	ENSG00000120738		"""Zinc fingers, C2H2-type"""	3238	protein-coding gene	gene with protein product	"""nerve growth factor-induced protein A"", ""transcription factor ETR103"", ""zinc finger protein 225"", ""early growth response protein 1"""	128990				3127059	Standard	NM_001964		Approved	TIS8, G0S30, NGFI-A, KROX-24, ZIF-268, AT225, ZNF225	uc003ldb.1	P18146	OTTHUMG00000129197	ENST00000239938.4:c.183_185delCAG	5.37:g.137801642_137801644delCAG	ENSP00000239938:p.Ser67del						p.NS61del	NM_001964.2	NP_001955.1	P18146	EGR1_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)		1	455_457	+			61			Gly/Ser-rich.			In_Frame_Del	DEL	ENST00000239938.4	37	c.183_185delCAG	CCDS4206.1																																																																																				0.700	EGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251274.1	NM_001964		8	272						8	272	---	---	---	---
CSF1R	1436	broad.mit.edu	37	5	149447806	149447808	+	In_Frame_Del	DEL	AGC	AGC	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr5:149447806_149447808delAGC	ENST00000286301.3	-	11	1887_1889	c.1596_1598delGCT	c.(1594-1599)ctgctc>ctc	p.532_533LL>L	CSF1R_ENST00000515239.1_5'Flank	NM_005211.3	NP_005202.2	P07333	CSF1R_HUMAN	colony stimulating factor 1 receptor	532					cell proliferation (GO:0008283)|cell-cell junction maintenance (GO:0045217)|cellular response to cytokine stimulus (GO:0071345)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cytokine-mediated signaling pathway (GO:0019221)|hemopoiesis (GO:0030097)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage differentiation (GO:0030225)|mammary gland duct morphogenesis (GO:0060603)|monocyte differentiation (GO:0030224)|multicellular organismal development (GO:0007275)|osteoclast differentiation (GO:0030316)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol metabolic process (GO:0046488)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell motility (GO:2000147)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of bone resorption (GO:0045124)|regulation of cell shape (GO:0008360)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|macrophage colony-stimulating factor receptor activity (GO:0005011)|protein homodimerization activity (GO:0042803)			NS(2)|breast(2)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(38)|kidney(2)|large_intestine(6)|liver(3)|lung(23)|ovary(2)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	93			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Imatinib(DB00619)|Sunitinib(DB01268)	Tagcagcaggagcagcagcagca	0.596																																						ENST00000286301.3																			0				NS(2)|breast(2)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(38)|kidney(2)|large_intestine(6)|liver(3)|lung(23)|ovary(2)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	93						c.(1594-1599)ctc>ct		colony stimulating factor 1 receptor	Imatinib(DB00619)|Sunitinib(DB01268)																																			SO:0001651	inframe_deletion	1436				cell proliferation|multicellular organismal development|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane|receptor complex	ATP binding|cytokine binding|macrophage colony-stimulating factor receptor activity|protein homodimerization activity	g.chr5:149447806_149447808delAGC	U63963	CCDS4302.1	5q32	2013-01-11	2008-08-01		ENSG00000182578	ENSG00000182578		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	2433	protein-coding gene	gene with protein product		164770	"""McDonough feline sarcoma viral (v-fms) oncogene homolog"""	FMS		1611909	Standard	NM_005211		Approved	C-FMS, CSFR, CD115	uc003lrm.3	P07333	OTTHUMG00000130050	ENST00000286301.3:c.1596_1598delGCT	5.37:g.149447815_149447817delAGC	ENSP00000286301:p.Leu537del						p.LL536del	NM_005211.3	NP_005202.2	P07333	CSF1R_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		11	1887_1889	-			536		L -> V (in dbSNP:rs55942044).			B5A955|D3DQG2|Q6LDW5|Q6LDY4|Q86VW7	In_Frame_Del	DEL	ENST00000286301.3	37	c.1596_1598delGCT	CCDS4302.1																																																																																				0.596	CSF1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252329.2	NM_005211		8	419						8	419	---	---	---	---
BTNL8	79908	broad.mit.edu	37	5	180338421	180338421	+	Frame_Shift_Del	DEL	C	C	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr5:180338421delC	ENST00000340184.4	+	3	686	c.480delC	c.(478-480)ttcfs	p.F160fs	BTNL8_ENST00000533815.2_5'UTR|Y_RNA_ENST00000410920.1_RNA|BTNL8_ENST00000231229.4_Frame_Shift_Del_p.F160fs|BTNL8_ENST00000400707.3_Frame_Shift_Del_p.F35fs|BTNL8_ENST00000505126.1_5'UTR|BTNL8_ENST00000511704.1_Frame_Shift_Del_p.F44fs|BTNL8_ENST00000508408.1_Frame_Shift_Del_p.F160fs	NM_001040462.2	NP_001035552.1	Q6UX41	BTNL8_HUMAN	butyrophilin-like 8	160	Ig-like V-type 2.				immune system process (GO:0002376)	integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(12)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	28	all_cancers(89;3.37e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CGGGCTGGTTCCCCCGGCCCA	0.532																																						ENST00000231229.4																			0				breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(12)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	28						c.(478-480)ttfs		butyrophilin-like 8							163.0	177.0	173.0					5																	180338421		2203	4296	6499	SO:0001589	frameshift_variant	79908					integral to membrane		g.chr5:180338421delC	AK025111	CCDS4459.1, CCDS43413.1, CCDS54956.1, CCDS54957.1, CCDS54958.1, CCDS54959.1	5q35.3	2014-01-14			ENSG00000113303	ENSG00000113303		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	26131	protein-coding gene	gene with protein product		615606				12975309	Standard	NM_024850		Approved	FLJ21458, BTN9.2	uc003mmp.3	Q6UX41	OTTHUMG00000130932	ENST00000340184.4:c.480delC	5.37:g.180338421delC	ENSP00000342197:p.Phe160fs					BTNL8_ENST00000505126.1_5'UTR|BTNL8_ENST00000400707.3_Frame_Shift_Del_p.F35fs|BTNL8_ENST00000340184.4_Frame_Shift_Del_p.F160fs|BTNL8_ENST00000533815.2_5'UTR|BTNL8_ENST00000511704.1_Frame_Shift_Del_p.F44fs|BTNL8_ENST00000508408.1_Frame_Shift_Del_p.F160fs	p.F160fs	NM_001159708.1|NM_024850.2	NP_001153180.1|NP_079126.1	Q6UX41	BTNL8_HUMAN	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		3	714	+	all_cancers(89;3.37e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	160			Ig-like V-type 2.		A4QMZ8|A6NEX6|B7Z409|B7Z5B1|E9PEF6|E9PG07|F2Z2B2|F8W712|Q9H730	Frame_Shift_Del	DEL	ENST00000340184.4	37	c.480delC	CCDS43413.1																																																																																				0.532	BTNL8-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368440.1	NM_024850		7	1276						7	1276	---	---	---	---
DEK	7913	broad.mit.edu	37	6	18264079	18264081	+	In_Frame_Del	DEL	TCC	TCC	-	rs377513079		TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr6:18264079_18264081delTCC	ENST00000397239.3	-	2	585_587	c.138_140delGGA	c.(136-141)gaggaa>gaa	p.46_47EE>E	DEK_ENST00000244776.7_In_Frame_Del_p.46_47EE>E	NM_003472.3	NP_003463.1	P35659	DEK_HUMAN	DEK proto-oncogene	46	Asp/Glu-rich (highly acidic).				chromatin modification (GO:0016568)|regulation of double-strand break repair (GO:2000779)|regulation of double-strand break repair via nonhomologous end joining (GO:2001032)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	7	Ovarian(93;0.00769)|Breast(50;0.0495)	all_hematologic(90;0.053)	OV - Ovarian serous cystadenocarcinoma(7;0.00291)|all cancers(50;0.031)|Epithelial(50;0.0332)			CCCACCTTTTtcctcctcctcct	0.532			T	NUP214	AML																																	ENST00000397239.3				Dom	yes		6	6p23	7913	T	DEK oncogene (DNA binding)			L	NUP214		AML		0				endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	7						c.(136-141)gaa>ga		DEK oncogene			,	77,1,4184		12,0,53,0,1,2065					,	-0.3	1.0			50	90,5,8159		17,0,56,0,5,4049	no	codingComplex,codingComplex	DEK	NM_003472.3,NM_001134709.1	,	29,0,109,0,6,6114	A1A1,A1A2,A1R,A2A2,A2R,RR		1.151,1.8301,1.3822	,	,		167,6,12343				SO:0001651	inframe_deletion	7913				chromatin modification|regulation of transcription from RNA polymerase II promoter|signal transduction|transcription from RNA polymerase II promoter|viral genome replication	nucleus	DNA binding|histone binding	g.chr6:18264079_18264081delTCC	X64229	CCDS34344.1, CCDS47382.1	6p23	2014-06-25	2014-06-25		ENSG00000124795	ENSG00000124795			2768	protein-coding gene	gene with protein product		125264	"""DEK oncogene (DNA binding)"", ""DEK oncogene"""			1549122	Standard	NM_003472		Approved	D6S231E	uc003ncr.1	P35659	OTTHUMG00000014319	ENST00000397239.3:c.138_140delGGA	6.37:g.18264088_18264090delTCC	ENSP00000380414:p.Glu47del					DEK_ENST00000244776.7_In_Frame_Del_p.EE46del	p.EE46del	NM_003472.3	NP_003463.1	P35659	DEK_HUMAN	OV - Ovarian serous cystadenocarcinoma(7;0.00291)|all cancers(50;0.031)|Epithelial(50;0.0332)		2	585_587	-	Ovarian(93;0.00769)|Breast(50;0.0495)	all_hematologic(90;0.053)	46			Asp/Glu-rich (highly acidic).		B2R6K6|B4DN37|Q5TGV4|Q5TGV5	In_Frame_Del	DEL	ENST00000397239.3	37	c.138_140delGGA	CCDS34344.1																																																																																				0.532	DEK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039962.4			8	477						8	477	---	---	---	---
HLA-F	3134	broad.mit.edu	37	6	29694802	29694803	+	IGR	INS	-	-	T	rs17875385		TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr6:29694802_29694803insT	ENST00000376861.1	+	0	1544				HLA-F_ENST00000259951.7_Frame_Shift_Ins_p.F394fs|HLA-F_ENST00000475996.1_Intron|HLA-F_ENST00000440587.2_Intron			P30511	HLAF_HUMAN	major histocompatibility complex, class I, F						antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)	early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)|TAP1 binding (GO:0046978)|TAP2 binding (GO:0046979)			cervix(1)|endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	8						TGTGGATCTTGTTTTTTTTGTG	0.535																																						ENST00000259951.7																			0				cervix(1)|endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	8						c.(1177-1182)ttttttfs		major histocompatibility complex, class I, F				16,3332		2,12,1660						-0.3	0.3		dbSNP_124	229	17,6555		4,9,3273	no	frameshift	HLA-F	NM_001098479.1		6,21,4933	A1A1,A1R,RR		0.2587,0.4779,0.3327				33,9887				SO:0001628	intergenic_variant	3134				antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|regulation of immune response|type I interferon-mediated signaling pathway	integral to membrane|MHC class I protein complex	MHC class I receptor activity	g.chr6:29694802_29694803insT	AY253269	CCDS43437.1, CCDS43438.1, CCDS43439.1	6p21.3	2013-01-11			ENSG00000204642	ENSG00000204642		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4963	protein-coding gene	gene with protein product		143110				1688605	Standard	NM_018950		Approved		uc003nno.4	P30511	OTTHUMG00000031156		6.37:g.29694810_29694810dupT						HLA-F_ENST00000475996.1_Intron|HLA-F_ENST00000440587.2_Intron	p.FF393fs	NM_001098479.1	NP_001091949.1	P30511	HLAF_HUMAN			7	1235_1236	+			0					Q5JQI8|Q5JQJ1|Q5SPT5|Q860R0|Q8MGQ1|Q8WLP5|Q95HC0|Q9TP68	Frame_Shift_Ins	INS	ENST00000376861.1	37	c.1179_1180insT	CCDS43438.1																																																																																				0.535	HLA-F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195083.1	NM_018950		30	1526						30	1526	---	---	---	---
TREML2	79865	broad.mit.edu	37	6	41168714	41168716	+	In_Frame_Del	DEL	CAG	CAG	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr6:41168714_41168716delCAG	ENST00000483722.1	-	1	216_218	c.31_33delCTG	c.(31-33)ctgdel	p.L11del		NM_024807.2	NP_079083.2	Q5T2D2	TRML2_HUMAN	triggering receptor expressed on myeloid cells-like 2	11					T cell activation (GO:0042110)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(1)|central_nervous_system(1)|large_intestine(1)|lung(13)|ovary(1)|prostate(1)	18	Ovarian(28;0.0418)|Colorectal(47;0.196)					CCTGTGGCCACAGCAGCAGCAGC	0.631																																						ENST00000483722.1																			0				breast(1)|central_nervous_system(1)|large_intestine(1)|lung(13)|ovary(1)|prostate(1)	18						c.(31-33)del		triggering receptor expressed on myeloid cells-like 2				143,4121		8,127,1997						4.0	1.0			26	249,8005		8,233,3886	no	coding	TREML2	NM_024807.2		16,360,5883	A1A1,A1R,RR		3.0167,3.3537,3.1315				392,12126				SO:0001651	inframe_deletion	79865				T cell activation	cell surface|integral to membrane|plasma membrane	protein binding|receptor activity	g.chr6:41168714_41168716delCAG	AK023755	CCDS4853.1, CCDS4853.2	6p21.1	2013-01-11	2004-04-14	2004-04-16	ENSG00000112195	ENSG00000112195		"""Immunoglobulin superfamily / V-set domain containing"""	21092	protein-coding gene	gene with protein product	"""TREM-like transcript 2"""	609715	"""chromosome 6 open reading frame 76"""	C6orf76		12645956	Standard	NM_024807		Approved	FLJ13693, TLT2, dJ238O23.1	uc010jxm.1	Q5T2D2	OTTHUMG00000016349	ENST00000483722.1:c.31_33delCTG	6.37:g.41168723_41168725delCAG	ENSP00000418767:p.Leu11del						p.L11del	NM_024807.2	NP_079083.2	Q5T2D2	TRML2_HUMAN			1	216_218	-	Ovarian(28;0.0418)|Colorectal(47;0.196)		11					Q08AP8|Q08AP9|Q8IWY0|Q9H8E9	In_Frame_Del	DEL	ENST00000483722.1	37	c.31_33delCTG	CCDS4853.2																																																																																				0.631	TREML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043756.3	NM_024807		8	214						8	214	---	---	---	---
GSTA1	2938	broad.mit.edu	37	6	52664097	52664100	+	Splice_Site	DEL	TGAA	TGAA	-	rs532349136|rs371582490|rs191668218	byFrequency	TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr6:52664097_52664100delTGAA	ENST00000334575.5	-	2	126		c.e2-2		GSTA1_ENST00000493331.1_5'Flank	NM_145740.3	NP_665683.1	P08263	GSTA1_HUMAN	glutathione S-transferase alpha 1						epithelial cell differentiation (GO:0030855)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|metabolic process (GO:0008152)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	glutathione transferase activity (GO:0004364)			large_intestine(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	12	Lung NSC(77;0.118)				Azathioprine(DB00993)|Busulfan(DB01008)|Glutathione(DB00143)	TCTCTAAGCCtgaatgaatgaatg	0.431														6	0.00119808	0.0	0.0	5008	,	,		20345	0.0		0.006	False		,,,				2504	0.0					ENST00000334575.5																			0				large_intestine(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	12						c.e2-2		glutathione S-transferase alpha 1	Amsacrine(DB00276)|Busulfan(DB01008)|Glutathione(DB00143)			25,4239		0,25,2107						-0.4	0.0			60	53,8201		0,53,4074	no	splice-3	GSTA1	NM_145740.3		0,78,6181	A1A1,A1R,RR		0.6421,0.5863,0.6231				78,12440				SO:0001630	splice_region_variant	2938				glutathione metabolic process|xenobiotic metabolic process	cytosol	glutathione transferase activity	g.chr6:52664097_52664100delTGAA		CCDS4945.1	6p12.2	2012-06-21	2008-11-26		ENSG00000243955	ENSG00000243955	2.5.1.18	"""Glutathione S-transferases / Soluble"""	4626	protein-coding gene	gene with protein product		138359	"""glutathione S-transferase A1"""			9503014	Standard	NM_145740		Approved		uc003paz.3	P08263	OTTHUMG00000014861	ENST00000334575.5:c.30-2TTCA>-	6.37:g.52664105_52664108delTGAA								NM_145740.3	NP_665683.1	P08263	GSTA1_HUMAN			2	126	-	Lung NSC(77;0.118)							Q14750|Q5GHF8|Q5SZC1	Splice_Site	DEL	ENST00000334575.5	37		CCDS4945.1																																																																																				0.431	GSTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040922.1		Intron	7	308						7	308	---	---	---	---
GABRR1	2569	broad.mit.edu	37	6	89891719	89891721	+	In_Frame_Del	DEL	AAG	AAG	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr6:89891719_89891721delAAG	ENST00000454853.2	-	8	962_964	c.852_854delCTT	c.(850-855)ttcttg>ttg	p.F284del	GABRR1_ENST00000435811.1_In_Frame_Del_p.F267del|GABRR1_ENST00000369451.3_In_Frame_Del_p.F197del	NM_001256704.1|NM_002042.4	NP_001243633.1|NP_002033.2	P24046	GBRR1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, rho 1	284					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(7)|lung(16)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	35		all_cancers(76;9.49e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.46e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;0.000114)		BRCA - Breast invasive adenocarcinoma(108;0.00917)	Adinazolam(DB00546)|Bromazepam(DB01558)|Cinolazepam(DB01594)|Clotiazepam(DB01559)|Diazepam(DB00829)|Estazolam(DB01215)|Fludiazepam(DB01567)|Flurazepam(DB00690)|Halazepam(DB00801)|Midazolam(DB00683)|Nitrazepam(DB01595)|Oxazepam(DB00842)|Prazepam(DB01588)|Quazepam(DB01589)|Temazepam(DB00231)|Triazolam(DB00897)	AGTTTGGAGCAAGAAGAAGAAGA	0.522																																						ENST00000435811.1																			0				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(7)|lung(16)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	35						c.(799-804)ttg>tt		gamma-aminobutyric acid (GABA) A receptor, rho 1	Picrotoxin(DB00466)																																			SO:0001651	inframe_deletion	2569				gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity	g.chr6:89891719_89891721delAAG		CCDS5019.2, CCDS59028.1, CCDS59029.1	6q15	2012-06-22	2012-02-03		ENSG00000146276	ENSG00000146276		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4090	protein-coding gene	gene with protein product	"""GABA(A) receptor, rho 1"""	137161	"""gamma-aminobutyric acid (GABA) receptor, rho 1"""			1849271, 1315307	Standard	NM_002042		Approved		uc003pna.2	P24046	OTTHUMG00000015195	ENST00000454853.2:c.852_854delCTT	6.37:g.89891728_89891730delAAG	ENSP00000412673:p.Phe284del					GABRR1_ENST00000369451.3_In_Frame_Del_p.FL197del|GABRR1_ENST00000454853.2_In_Frame_Del_p.FL284del	p.FL267del	NM_001256703.1	NP_001243632.1	P24046	GBRR1_HUMAN		BRCA - Breast invasive adenocarcinoma(108;0.00917)	7	1255_1257	-		all_cancers(76;9.49e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.46e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;0.000114)	284					A1L401|B4DJK8|B4DQT5|B7ZBQ7|Q9BX06	In_Frame_Del	DEL	ENST00000454853.2	37	c.801_803delCTT	CCDS5019.2																																																																																				0.522	GABRR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041479.2			7	531						7	531	---	---	---	---
FYN	2534	broad.mit.edu	37	6	111983042	111983042	+	Frame_Shift_Del	DEL	T	T	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr6:111983042delT	ENST00000354650.3	-	14	2120	c.1514delA	c.(1513-1515)aagfs	p.K505fs	FYN_ENST00000368682.3_Frame_Shift_Del_p.K502fs|FYN_ENST00000538466.1_Frame_Shift_Del_p.K502fs|FYN_ENST00000356013.2_Frame_Shift_Del_p.K450fs|FYN_ENST00000368667.2_Frame_Shift_Del_p.K505fs|FYN_ENST00000368678.4_Frame_Shift_Del_p.K502fs|FYN_ENST00000229470.5_Frame_Shift_Del_p.K453fs|FYN_ENST00000229471.4_Frame_Shift_Del_p.K450fs	NM_002037.5	NP_002028.1	P06241	FYN_HUMAN	FYN proto-oncogene, Src family tyrosine kinase	505	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activated T cell proliferation (GO:0050798)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|cellular response to peptide hormone stimulus (GO:0071375)|dendrite morphogenesis (GO:0048813)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|feeding behavior (GO:0007631)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain development (GO:0030900)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning (GO:0007612)|leukocyte migration (GO:0050900)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of gene expression (GO:0010629)|negative regulation of protein catabolic process (GO:0042177)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein localization to nucleus (GO:1900182)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell shape (GO:0008360)|regulation of defense response to virus by virus (GO:0050690)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cytosol (GO:0005829)|endosome (GO:0005768)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	ATP binding (GO:0005524)|ephrin receptor binding (GO:0046875)|glycoprotein binding (GO:0001948)|growth factor receptor binding (GO:0070851)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(17)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	30		all_cancers(87;1.37e-05)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.00125)|Colorectal(196;0.0211)		all cancers(137;0.0451)|OV - Ovarian serous cystadenocarcinoma(136;0.0476)|Epithelial(106;0.102)	Dasatinib(DB01254)	TTCAGGGTCCTTTTTCCAGCA	0.562																																						ENST00000354650.3																			0				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(17)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	30						c.(1513-1515)agfs		FYN oncogene related to SRC, FGR, YES	Dasatinib(DB01254)						150.0	156.0	154.0					6																	111983042		2203	4300	6503	SO:0001589	frameshift_variant	2534				axon guidance|calcium ion transport|feeding behavior|interspecies interaction between organisms|intracellular protein kinase cascade|learning|leukocyte migration|platelet activation|regulation of defense response to virus by virus|T cell costimulation|T cell receptor signaling pathway|viral reproduction	cytosol|endosome|plasma membrane	ATP binding|glycoprotein binding|identical protein binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity	g.chr6:111983042delT	AK056699	CCDS5094.1, CCDS5095.1, CCDS5096.1	6q21	2014-06-25	2014-06-25		ENSG00000010810	ENSG00000010810		"""SH2 domain containing"""	4037	protein-coding gene	gene with protein product		137025	"""FYN oncogene related to SRC, FGR, YES"""			3526330	Standard	NM_002037		Approved	SYN, SLK, MGC45350	uc003pvh.3	P06241	OTTHUMG00000016305	ENST00000354650.3:c.1514delA	6.37:g.111983042delT	ENSP00000346671:p.Lys505fs					FYN_ENST00000229471.4_Frame_Shift_Del_p.K450fs|FYN_ENST00000368678.4_Frame_Shift_Del_p.K502fs|FYN_ENST00000229470.5_Frame_Shift_Del_p.K453fs|FYN_ENST00000368667.2_Frame_Shift_Del_p.K505fs|FYN_ENST00000356013.2_Frame_Shift_Del_p.K450fs|FYN_ENST00000538466.1_Frame_Shift_Del_p.K502fs|FYN_ENST00000368682.3_Frame_Shift_Del_p.K502fs	p.K505fs	NM_002037.5	NP_002028.1	P06241	FYN_HUMAN		all cancers(137;0.0451)|OV - Ovarian serous cystadenocarcinoma(136;0.0476)|Epithelial(106;0.102)	14	2120	-		all_cancers(87;1.37e-05)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.00125)|Colorectal(196;0.0211)	505			Protein kinase.		B5BU57|E1P557|H0UI48|Q16248|Q5R3A6|Q5R3A7|Q8N5D7	Frame_Shift_Del	DEL	ENST00000354650.3	37	c.1514delA	CCDS5094.1																																																																																				0.562	FYN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043655.1			7	1267						7	1267	---	---	---	---
PHACTR2	9749	broad.mit.edu	37	6	144081695	144081696	+	Frame_Shift_Ins	INS	-	-	A			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr6:144081695_144081696insA	ENST00000427704.2	+	5	709_710	c.579_580insA	c.(580-582)aaafs	p.K194fs	PHACTR2_ENST00000367582.3_Intron|PHACTR2_ENST00000305766.6_Intron|PHACTR2_ENST00000367584.4_Intron|PHACTR2_ENST00000440869.2_Frame_Shift_Ins_p.K205fs	NM_001100166.1|NM_014721.2	NP_001093636.1|NP_055536.2	O75167	PHAR2_HUMAN	phosphatase and actin regulator 2	194							protein phosphatase inhibitor activity (GO:0004864)			NS(3)|breast(1)|cervix(1)|endometrium(3)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	30				OV - Ovarian serous cystadenocarcinoma(155;1.58e-05)|GBM - Glioblastoma multiforme(68;0.0386)		TGCCTCCCATTAAAAAAAATAC	0.569																																					Pancreas(12;292 433 7358 48260 52635)|Ovarian(20;501 618 3485 36581 49208)	ENST00000427704.2																			0				NS(3)|breast(1)|cervix(1)|endometrium(3)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	30						c.(577-582)ataaaafs		phosphatase and actin regulator 2																																				SO:0001589	frameshift_variant	9749						actin binding|protein phosphatase inhibitor activity	g.chr6:144081695_144081696insA	AB014580	CCDS43512.1, CCDS47492.1, CCDS47493.1, CCDS47494.1	6q24.1	2013-01-24	2004-05-20	2004-05-20	ENSG00000112419	ENSG00000112419		"""Phosphatase and actin regulators"""	20956	protein-coding gene	gene with protein product		608724	"""chromosome 6 open reading frame 56"""	C6orf56		9734811, 15107502	Standard	NM_001100164		Approved	KIAA0680	uc010khi.3	O75167	OTTHUMG00000015732	ENST00000427704.2:c.587dupA	6.37:g.144081703_144081703dupA	ENSP00000391763:p.Lys194fs					PHACTR2_ENST00000367582.3_Intron|PHACTR2_ENST00000305766.6_Intron|PHACTR2_ENST00000367584.4_Intron|PHACTR2_ENST00000440869.2_Frame_Shift_Ins_p.IK204fs	p.IK193fs	NM_001100166.1|NM_014721.2	NP_001093636.1|NP_055536.2	O75167	PHAR2_HUMAN		OV - Ovarian serous cystadenocarcinoma(155;1.58e-05)|GBM - Glioblastoma multiforme(68;0.0386)	5	709_710	+			193					A6NKP5|A7MCZ5|A8MZC0|B2RWP7|B4DN76|B4DPB5|B4DTH7|Q5TFA0|Q68DM2	Frame_Shift_Ins	INS	ENST00000427704.2	37	c.579_580insA	CCDS47492.1																																																																																				0.569	PHACTR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042528.2	NM_014721		9	425						9	425	---	---	---	---
GRM1	2911	broad.mit.edu	37	6	146755630	146755632	+	In_Frame_Del	DEL	GAC	GAC	-	rs568155311		TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr6:146755630_146755632delGAC	ENST00000282753.1	+	8	3518_3520	c.3283_3285delGAC	c.(3283-3285)gacdel	p.D1099del	GRM1_ENST00000361719.2_In_Frame_Del_p.D1099del|GRM1_ENST00000392299.2_3'UTR|GRM1_ENST00000507907.1_3'UTR|GRM1_ENST00000492807.2_3'UTR|GRM1_ENST00000355289.4_3'UTR			Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1	1099	Asp/Glu-rich (acidic).				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|cell death (GO:0008219)|cellular response to electrical stimulus (GO:0071257)|dimeric G-protein coupled receptor signaling pathway (GO:0038042)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of pain (GO:0019233)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|G-protein coupled receptor dimeric complex (GO:0038037)|G-protein coupled receptor homodimeric complex (GO:0038038)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)			NS(2)|breast(5)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(54)|ovary(7)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	126		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)		CCCGCCCGCGGACGACGACGACG	0.65																																						ENST00000361719.2																			0				NS(2)|breast(5)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(54)|ovary(7)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	126						c.(3283-3285)del		glutamate receptor, metabotropic 1	Acamprosate(DB00659)|L-Glutamic Acid(DB00142)																																			SO:0001651	inframe_deletion	2911				synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity	g.chr6:146755630_146755632delGAC	U31215	CCDS5209.1, CCDS47497.1, CCDS64548.1	6q24	2014-06-12			ENSG00000152822	ENSG00000152822		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4593	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 85"""	604473				9076744, 9376535	Standard	NM_001278064		Approved	GPRC1A, mGlu1, MGLUR1, PPP1R85	uc010khw.2	Q13255	OTTHUMG00000015752	ENST00000282753.1:c.3283_3285delGAC	6.37:g.146755639_146755641delGAC	ENSP00000282753:p.Asp1099del					GRM1_ENST00000507907.1_3'UTR|GRM1_ENST00000355289.4_3'UTR|GRM1_ENST00000392299.2_3'UTR|GRM1_ENST00000282753.1_In_Frame_Del_p.D1099del|GRM1_ENST00000492807.2_3'UTR	p.D1099del	NM_001278064.1	NP_001264993.1	Q13255	GRM1_HUMAN		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)	9	3753_3755	+		Ovarian(120;0.0387)	1099			Asp/Glu-rich (acidic).		B9EG79|F8W805|Q13256|Q14757|Q14758|Q5VTF7|Q5VTF8|Q9NU10|Q9UGS9|Q9UGT0	In_Frame_Del	DEL	ENST00000282753.1	37	c.3283_3285delGAC	CCDS5209.1																																																																																				0.650	GRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042574.1	NM_000838		7	765						7	765	---	---	---	---
TMEM184A	202915	broad.mit.edu	37	7	1586662	1586663	+	In_Frame_Ins	INS	-	-	GCC	rs3837151|rs3779607	byFrequency	TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr7:1586662_1586663insGCC	ENST00000297477.5	-	9	1483_1484	c.1167_1168insGGC	c.(1165-1170)cccagc>cccGGCagc	p.389_390PS>PGS	TMEM184A_ENST00000449955.1_5'Flank	NM_001097620.1	NP_001091089.1	Q6ZMB5	T184A_HUMAN	transmembrane protein 184A	389			S -> G (in dbSNP:rs3779607). {ECO:0000269|PubMed:15489334}.		germ-line sex determination (GO:0018992)|regulation of protein localization (GO:0032880)|regulation of secretion (GO:0051046)	early endosome membrane (GO:0031901)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	12		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;5.88e-15)		GAGCCGCCGCTGGGGTGGGTGC	0.703																																						ENST00000297477.5																			0				endometrium(1)|large_intestine(1)|lung(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	12						c.(1165-1170)ccgcgg>ccGGCgcgg		transmembrane protein 184A				1912,2170		535,842,664						-3.6	0.0		dbSNP_132	17	3872,4214		1028,1816,1199	no	coding	TMEM184A	NM_001097620.1		1563,2658,1863	A1A1,A1R,RR		47.8852,46.8398,47.5345				5784,6384				SO:0001652	inframe_insertion	202915					integral to membrane		g.chr7:1586662_1586663insGCC		CCDS43537.1	7p22.3	2008-05-02			ENSG00000164855	ENSG00000164855			28797	protein-coding gene	gene with protein product						12477932	Standard	NM_001097620		Approved	MGC9712	uc003skv.4	Q6ZMB5	OTTHUMG00000119025	ENST00000297477.5:c.1167_1168insGGC	7.37:g.1586662_1586663insGCC	ENSP00000297477:p.Pro389_Ser390insGly						p.389_390PR>PAR	NM_001097620.1	NP_001091089.1	Q6ZMB5	T184A_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;5.88e-15)	9	1483_1484	-		Ovarian(82;0.0253)	389					Q8TBQ6	In_Frame_Ins	INS	ENST00000297477.5	37	c.1167_1168insGGC	CCDS43537.1																																																																																				0.703	TMEM184A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239229.4	NM_152689		12	198						12	198	---	---	---	---
CCT6P3	643180	broad.mit.edu	37	7	64528813	64528814	+	RNA	INS	-	-	T			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr7:64528813_64528814insT	ENST00000426828.1	+	0	621				SNORA22_ENST00000384614.1_RNA|SNORA15_ENST00000384334.1_RNA	NR_033416.1				chaperonin containing TCP1, subunit 6 (zeta) pseudogene 3																		CTTTCTGTAACTTTTTTTTTTT	0.317																																						ENST00000426828.1																			0																																																			0							g.chr7:64528813_64528814insT			7q11.21	2010-06-29			ENSG00000234585	ENSG00000234585			35137	pseudogene	pseudogene							Standard	NR_033416		Approved		uc010kzt.1		OTTHUMG00000156630		7.37:g.64528824_64528824dupT								NR_033416.1						0	621	+									RNA	INS	ENST00000426828.1	37																																																																																						0.317	CCT6P3-004	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000344862.1			7	91						7	91	---	---	---	---
INTS4L2	644619	broad.mit.edu	37	7	65150816	65150816	+	RNA	DEL	A	A	-	rs376935907		TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr7:65150816delA	ENST00000430126.2	+	0	757							Q2T9F4	IN4L2_HUMAN	integrator complex subunit 4-like 2																		TTCATCCCTCACCCCCCCCCC	0.463																																						ENST00000430126.2																			0																																																			0							g.chr7:65150816delA	BC111554		7q11.21	2013-03-26			ENSG00000232270	ENSG00000273024			22351	other	unknown							Standard	NR_027392		Approved	MGC133166	uc003tue.2	Q2T9F4	OTTHUMG00000156558		7.37:g.65150816delA														0	757	+									RNA	DEL	ENST00000430126.2	37																																																																																						0.463	INTS4L2-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000345545.2	NR_027392		15	103						15	103	---	---	---	---
TYW1B	441250	broad.mit.edu	37	7	72040750	72040751	+	RNA	INS	-	-	A			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr7:72040750_72040751insA	ENST00000435769.2	-	0	1909				TYW1B_ENST00000438125.1_RNA|TYW1B_ENST00000343721.5_RNA			Q6NUM6	TYW1B_HUMAN	tRNA-yW synthesizing protein 1 homolog B (S. cerevisiae)						tRNA processing (GO:0008033)		4 iron, 4 sulfur cluster binding (GO:0051539)|FMN binding (GO:0010181)|iron ion binding (GO:0005506)|lyase activity (GO:0016829)|oxidoreductase activity (GO:0016491)										AACATCCCTAGAAAAAAAAAAT	0.332																																						ENST00000438125.1																			0													tRNA-yW synthesizing protein 1 homolog B (S. cerevisiae)																																						441250				tRNA processing		4 iron, 4 sulfur cluster binding|FMN binding|iron ion binding|oxidoreductase activity	g.chr7:72040750_72040751insA	BC068520	CCDS69309.1	7q11.23	2011-08-11	2009-07-28		ENSG00000254184	ENSG00000277149			33908	protein-coding gene	gene with protein product	"""radical S-adenosyl methionine and flavodoxin domains 1"", ""non-protein coding RNA 69"", ""long intergenic non-protein coding RNA 69"""		"""tRNA-yW synthesizing protein 1 homolog B (non-protein coding)"""				Standard	NM_001145440		Approved	RSAFD2, MGC87315, NCRNA00069, LINC00069	uc011kej.2	Q6NUM6	OTTHUMG00000157067		7.37:g.72040760_72040760dupA										Q6NUM6	TYW1B_HUMAN			0	1399	-								A6NG09|B4DFY2|Q3KQX2	RNA	INS	ENST00000435769.2	37																																																																																						0.332	TYW1B-001	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000347346.2	NM_001145440		9	204						9	204	---	---	---	---
AKAP9	10142	broad.mit.edu	37	7	91671392	91671393	+	Frame_Shift_Del	DEL	AG	AG	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr7:91671392_91671393delAG	ENST00000359028.2	+	20	5211_5212	c.4986_4987delAG	c.(4984-4989)tcagagfs	p.E1663fs	AKAP9_ENST00000358100.2_Frame_Shift_Del_p.E1663fs|AKAP9_ENST00000356239.3_Frame_Shift_Del_p.E1651fs			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	1663					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)			NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			ACCTGGTTTCAGAGAGAGAGAG	0.411			T	BRAF	papillary thyroid																																	ENST00000359028.2				Dom	yes		7	7q21-q22	10142	T	A kinase (PRKA) anchor protein (yotiao) 9			E	BRAF		papillary thyroid		0				NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155						c.(4984-4989)tcagfs		A kinase (PRKA) anchor protein 9																																				SO:0001589	frameshift_variant	10142				G2/M transition of mitotic cell cycle|signal transduction|synaptic transmission|transport	centrosome|cytosol|Golgi apparatus	receptor binding	g.chr7:91671392_91671393delAG	AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	379	protein-coding gene	gene with protein product	"""A-kinase anchoring protein 450"", ""AKAP9-BRAF fusion protein"", ""AKAP120-like protein"", ""centrosome- and golgi-localized protein kinase N-associated protein"", ""protein kinase A anchoring protein 9"", ""A-kinase anchor protein, 350kDa"", ""protein phosphatase 1, regulatory subunit 45"", ""yotiao"""	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.4986_4987delAG	7.37:g.91671402_91671403delAG	ENSP00000351922:p.Glu1663fs					AKAP9_ENST00000358100.2_Frame_Shift_Del_p.SE1662fs|AKAP9_ENST00000356239.3_Frame_Shift_Del_p.SE1650fs	p.SE1662fs			Q99996	AKAP9_HUMAN	STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)		20	5211_5212	+	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		1662					A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Frame_Shift_Del	DEL	ENST00000359028.2	37	c.4986_4987delAG																																																																																					0.411	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751		9	304						9	304	---	---	---	---
MEPCE	56257	broad.mit.edu	37	7	100028823	100028825	+	In_Frame_Del	DEL	CCA	CCA	-	rs71555278		TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr7:100028823_100028825delCCA	ENST00000310512.2	+	1	1570_1572	c.1182_1184delCCA	c.(1180-1185)cgccac>cgc	p.H399del	ZCWPW1_ENST00000360951.4_5'Flank|ZCWPW1_ENST00000324725.6_5'Flank|MEPCE_ENST00000414441.1_5'UTR|ZCWPW1_ENST00000398027.2_5'Flank	NM_019606.5	NP_062552.2	Q7L2J0	MEPCE_HUMAN	methylphosphate capping enzyme	399					negative regulation of chromatin binding (GO:0035562)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|RNA methylation (GO:0001510)|snRNA metabolic process (GO:0016073)|snRNA modification (GO:0040031)		poly(A) RNA binding (GO:0044822)|RNA methyltransferase activity (GO:0008173)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|liver(2)|lung(9)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	24	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GGGGAGGCCGCCACCACCACCAC	0.581																																						ENST00000310512.2																			0				breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|liver(2)|lung(9)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	24						c.(1180-1185)cgc>cg		methylphosphate capping enzyme																																				SO:0001651	inframe_deletion	56257						methyltransferase activity	g.chr7:100028823_100028825delCCA	AF264752	CCDS5693.1, CCDS55136.1	7q22.1	2008-02-04	2007-07-26	2007-07-26	ENSG00000146834	ENSG00000146834			20247	protein-coding gene	gene with protein product		611478	"""bin3, bicoid-interacting 3, homolog (Drosophila)"""	BCDIN3		12358911, 17643375	Standard	NM_019606		Approved	FLJ20257, MePCE	uc003uuw.3	Q7L2J0	OTTHUMG00000155255	ENST00000310512.2:c.1182_1184delCCA	7.37:g.100028832_100028834delCCA	ENSP00000308546:p.His399del					MEPCE_ENST00000414441.1_5'UTR	p.RH394del	NM_019606.5	NP_062552.2	Q7L2J0	MEPCE_HUMAN			1	1570_1572	+	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)		394					B3KP86|D6W5V7|Q9NPD4	In_Frame_Del	DEL	ENST00000310512.2	37	c.1182_1184delCCA	CCDS5693.1																																																																																				0.581	MEPCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339135.1			8	482						8	482	---	---	---	---
SRRT	51593	broad.mit.edu	37	7	100479332	100479332	+	Frame_Shift_Del	DEL	G	G	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr7:100479332delG	ENST00000347433.4	+	4	462	c.304delG	c.(304-306)gggfs	p.G106fs	SRRT_ENST00000457580.2_Frame_Shift_Del_p.G106fs|SRRT_ENST00000388793.4_Frame_Shift_Del_p.G106fs|SRRT_ENST00000432932.1_Frame_Shift_Del_p.G106fs			Q9BXP5	SRRT_HUMAN	serrate, RNA effector molecule	106				G -> GG (in Ref. 3; CAB46374). {ECO:0000305}.	cell proliferation (GO:0008283)|neuronal stem cell maintenance (GO:0097150)|primary miRNA processing (GO:0031053)|regulation of transcription, DNA-templated (GO:0006355)|response to arsenic-containing substance (GO:0046685)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)	p.G104fs*45(1)		breast(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(5)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	40						GCCCTATGCTGGGGGGGGTGG	0.607																																						ENST00000388793.4																			1	Deletion - Frameshift(1)	p.G104fs*45(1)	ovary(1)	breast(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(5)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	40						c.(304-306)ggfs		serrate RNA effector molecule homolog (Arabidopsis)			,,,	57,63,4112		1,0,55,5,53,2002	29.0	30.0	30.0		,,,	4.3	1.0	7		30	49,115,8030		0,0,49,12,91,3945	no	codingComplex,codingComplex,codingComplex,codingComplex	SRRT	NM_015908.5,NM_001128854.1,NM_001128853.1,NM_001128852.1	,,,	1,0,104,17,144,5947	A1A1,A1A2,A1R,A2A2,A2R,RR		2.0015,2.8355,2.2855	,,,	,,,	100479332	106,178,12142	2197	4287	6484	SO:0001589	frameshift_variant	51593				cell proliferation|primary miRNA processing|response to arsenic-containing substance	cytoplasm|nucleoplasm	protein binding	g.chr7:100479332delG		CCDS34709.1, CCDS47665.1, CCDS47666.1, CCDS47667.1	7q21	2014-04-14	2014-04-14		ENSG00000087087	ENSG00000087087			24101	protein-coding gene	gene with protein product	"""arsenite resistance protein"""	614469	"""serrate RNA effector molecule homolog (Arabidopsis)"""			11239002, 11230166	Standard	NM_015908		Approved	Asr2, serrate, ARS2	uc003uwy.2	Q9BXP5	OTTHUMG00000157031	ENST00000347433.4:c.304delG	7.37:g.100479332delG	ENSP00000314491:p.Gly106fs					SRRT_ENST00000457580.2_Frame_Shift_Del_p.G106fs|SRRT_ENST00000347433.4_Frame_Shift_Del_p.G106fs|SRRT_ENST00000432932.1_Frame_Shift_Del_p.G106fs	p.G106fs	NM_001128852.1|NM_015908.5	NP_001122324.1|NP_056992.4	Q9BXP5	SRRT_HUMAN			4	524	+			106	G -> GG (in Ref. 3; CAB46374).				A4D2E5|A4D2E6|A6NK22|B4DJL4|B4DZA6|O95808|Q32MI4|Q6NT74|Q8TDQ5|Q9BWP6|Q9BXP4|Q9Y4S4	Frame_Shift_Del	DEL	ENST00000347433.4	37	c.304delG	CCDS34709.1																																																																																				0.607	SRRT-004	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347168.1	NM_015908		7	260						7	260	---	---	---	---
FOXP2	93986	broad.mit.edu	37	7	114270016	114270018	+	In_Frame_Del	DEL	CAG	CAG	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr7:114270016_114270018delCAG	ENST00000393494.2	+	5	832_834	c.553_555delCAG	c.(553-555)cagdel	p.Q191del	FOXP2_ENST00000390668.3_In_Frame_Del_p.Q215del|AC020606.1_ENST00000580664.1_RNA|FOXP2_ENST00000350908.4_In_Frame_Del_p.Q191del|FOXP2_ENST00000393498.2_In_Frame_Del_p.Q171del|FOXP2_ENST00000403559.4_In_Frame_Del_p.Q208del|FOXP2_ENST00000408937.3_In_Frame_Del_p.Q216del|FOXP2_ENST00000393491.3_In_Frame_Del_p.Q99del|FOXP2_ENST00000393500.3_In_Frame_Del_p.Q116del|FOXP2_ENST00000360232.4_In_Frame_Del_p.Q191del|FOXP2_ENST00000378237.3_In_Frame_Del_p.Q191del|FOXP2_ENST00000393489.3_In_Frame_Del_p.Q99del			O15409	FOXP2_HUMAN	forkhead box P2	191	Gln-rich.				camera-type eye development (GO:0043010)|caudate nucleus development (GO:0021757)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|growth (GO:0040007)|lung alveolus development (GO:0048286)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of mesenchymal cell proliferation (GO:0002053)|post-embryonic development (GO:0009791)|putamen development (GO:0021758)|righting reflex (GO:0060013)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|vocal learning (GO:0042297)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|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)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Q210Q(2)		breast(3)|endometrium(7)|kidney(4)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	52						gcagcagcaacagcagcagcagc	0.507																																						ENST00000393500.3																			2	Substitution - coding silent(2)	p.Q210Q(2)	lung(2)	breast(3)|endometrium(7)|kidney(4)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	52						c.(328-330)del		forkhead box P2																																				SO:0001651	inframe_deletion	93986				camera-type eye development|caudate nucleus development|cerebellum development|cerebral cortex development|embryo development|growth|lung alveolus development|negative regulation of transcription, DNA-dependent|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of mesenchymal cell proliferation|post-embryonic development|putamen development|regulation of sequence-specific DNA binding transcription factor activity|righting reflex|skeletal muscle tissue development|smooth muscle tissue development|vocal learning	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding	g.chr7:114270016_114270018delCAG	U80741	CCDS5760.1, CCDS5761.1, CCDS43635.1, CCDS5761.2, CCDS55154.1	7q31	2008-07-18			ENSG00000128573	ENSG00000128573		"""Forkhead boxes"""	13875	protein-coding gene	gene with protein product	"""trinucleotide repeat containing 10"", ""forkhead/winged-helix transcription factor"", ""speech and language disorder 1"", ""CAG repeat protein 44"""	605317		TNRC10, SPCH1		11586359, 9225980	Standard	NM_014491		Approved	CAGH44	uc003vgz.3	O15409	OTTHUMG00000023131	ENST00000393494.2:c.553_555delCAG	7.37:g.114270025_114270027delCAG	ENSP00000377132:p.Gln191del					FOXP2_ENST00000390668.3_In_Frame_Del_p.Q215del|FOXP2_ENST00000393489.3_In_Frame_Del_p.Q99del|FOXP2_ENST00000378237.3_In_Frame_Del_p.Q191del|FOXP2_ENST00000360232.4_In_Frame_Del_p.Q191del|FOXP2_ENST00000408937.3_In_Frame_Del_p.Q216del|FOXP2_ENST00000393491.3_In_Frame_Del_p.Q99del|FOXP2_ENST00000393494.2_In_Frame_Del_p.Q191del|FOXP2_ENST00000403559.4_In_Frame_Del_p.Q208del|FOXP2_ENST00000350908.4_In_Frame_Del_p.Q191del|FOXP2_ENST00000393498.2_In_Frame_Del_p.Q171del	p.Q116del			O15409	FOXP2_HUMAN			11	1148_1150	+			191			Gln-rich.		A0AUV6|A4D0U8|A6NNW4|B4DLD9|Q6ZND1|Q75MJ3|Q8IZE0|Q8N0W2|Q8N6B7|Q8N6B8|Q8NFQ1|Q8NFQ2|Q8NFQ3|Q8NFQ4|Q8TD74	In_Frame_Del	DEL	ENST00000393494.2	37	c.328_330delCAG	CCDS5760.1																																																																																				0.507	FOXP2-014	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317366.1	NM_014491		7	423						7	423	---	---	---	---
OR9A4	130075	broad.mit.edu	37	7	141619203	141619203	+	Frame_Shift_Del	DEL	T	T	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr7:141619203delT	ENST00000548136.1	+	1	587	c.528delT	c.(526-528)aatfs	p.N176fs	MGAM_ENST00000497554.1_Intron	NM_001001656.1	NP_001001656.1	Q8NGU2	OR9A4_HUMAN	olfactory receptor, family 9, subfamily A, member 4	176						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(2)|large_intestine(9)|lung(7)|prostate(1)|skin(2)	22	Melanoma(164;0.0171)					TGGTGAACAATTTTTTTTGTG	0.383																																						ENST00000548136.1																			0				NS(1)|endometrium(2)|large_intestine(9)|lung(7)|prostate(1)|skin(2)	22						c.(526-528)aafs		olfactory receptor, family 9, subfamily A, member 4							152.0	152.0	152.0					7																	141619203		2056	4243	6299	SO:0001589	frameshift_variant	130075				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr7:141619203delT		CCDS43661.1	7q34	2012-10-03			ENSG00000258083	ENSG00000258083		"""GPCR / Class A : Olfactory receptors"""	15095	protein-coding gene	gene with protein product							Standard	NM_001001656		Approved		uc003vwu.1	Q8NGU2	OTTHUMG00000158370	ENST00000548136.1:c.528delT	7.37:g.141619203delT	ENSP00000448789:p.Asn176fs					MGAM_ENST00000497554.1_Intron	p.N176fs	NM_001001656.1	NP_001001656.1	Q8NGU2	OR9A4_HUMAN			1	587	+	Melanoma(164;0.0171)		176					B9EGV6|Q6IFI4	Frame_Shift_Del	DEL	ENST00000548136.1	37	c.528delT	CCDS43661.1																																																																																				0.383	OR9A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350806.3	NM_001001656		11	1081						11	1081	---	---	---	---
TRBV7-8	28590	broad.mit.edu	37	7	142099832	142099833	+	RNA	DEL	CA	CA	-	rs377589241|rs150299545|rs527701975	byFrequency	TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr7:142099832_142099833delCA	ENST00000390359.3	-	0	88									T cell receptor beta variable 7-8																		accactctctcacacacacaca	0.455																																						ENST00000390359.3																			0																	68,3612		7,54,1779						-5.2	0.0			58	51,7855		15,21,3917	no	intergenic				22,75,5696	A1A1,A1R,RR		0.6451,1.8478,1.0271				119,11467						0							g.chr7:142099832_142099833delCA	M11953		7q34	2012-02-07			ENSG00000229200			"""T cell receptors / TRB locus"""	12242	other	T cell receptor gene						8650574	Standard	NG_001333		Approved	TRBV78, TCRBV6S2A1N1T, TCRBV7S8			OTTHUMG00000158875		7.37:g.142099842_142099843delCA														0	88	-									RNA	DEL	ENST00000390359.3	37																																																																																						0.455	TRBV7-8-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	TR_V_gene	TR_V_gene	OTTHUMT00000352483.1	NG_001333		9	352						9	352	---	---	---	---
SSPO	23145	broad.mit.edu	37	7	149515189	149515189	+	RNA	DEL	A	A	-	rs60594151	byFrequency	TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr7:149515189delA	ENST00000378016.2	+	0	11577							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			GACCTCGAGTAACTGCCCCAG	0.667													A|AA|A|insertion	1839	0.367212	0.4402	0.3473	5008	,	,		16407	0.4206		0.2942	False		,,,				2504	0.3027					ENST00000378016.2																			0													SCO-spondin				1497,2307		384,729,789	5.0	7.0	6.0			1.8	0.2	7	dbSNP_132	8	2537,5339		482,1573,1883	no	frameshift	SSPO	NM_198455.2		866,2302,2672	A1A1,A1R,RR		32.2118,39.3533,34.5377			149515189	4034,7646	1638	3723	5361			23145				cell adhesion	extracellular space	peptidase inhibitor activity	g.chr7:149515189delA	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"""subcommissural organ spondin"", ""SCO protein, thrombospondin domain containing"""		"""SCO-spondin homolog (Bos taurus)"""			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149515189delA										A2VEC9	SSPO_HUMAN	OV - Ovarian serous cystadenocarcinoma(82;0.00625)		0	11577	+	Melanoma(164;0.165)|Ovarian(565;0.177)							Q76B61	RNA	DEL	ENST00000378016.2	37																																																																																						0.667	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				31	28						31	28	---	---	---	---
BMP1	649	broad.mit.edu	37	8	22021060	22021061	+	5'Flank	DEL	GT	GT	-	rs149538549		TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr8:22021060_22021061delGT	ENST00000306385.5	+	0	0				SFTPC_ENST00000522109.1_Frame_Shift_Del_p.V146fs|BMP1_ENST00000306349.8_5'Flank|SFTPC_ENST00000318561.3_Splice_Site|BMP1_ENST00000397814.3_5'Flank|SFTPC_ENST00000521315.1_Splice_Site|SFTPC_ENST00000437090.2_Splice_Site|SFTPC_ENST00000520605.1_Splice_Site|SFTPC_ENST00000524255.1_Splice_Site|BMP1_ENST00000397816.3_5'Flank|BMP1_ENST00000354870.5_5'Flank	NM_006129.4	NP_006120.1	P13497	BMP1_HUMAN	bone morphogenetic protein 1						cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|lipoprotein metabolic process (GO:0042157)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of cartilage development (GO:0061036)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane-bounded vesicle (GO:0031988)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)|zinc ion binding (GO:0008270)	p.M146fs*41(1)		breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(3)	30				Colorectal(74;0.00229)|COAD - Colon adenocarcinoma(73;0.0661)|READ - Rectum adenocarcinoma(644;0.11)		CAACTTCCAGGTGTGTGTGTGT	0.545																																						ENST00000522109.1																			1	Unknown(1)	p.M146fs*41(1)	large_intestine(1)	autonomic_ganglia(1)|large_intestine(1)|lung(1)	3	GRCh37	CS014615|CS022505	SFTPC	S	rs149538549	c.(436-438)gfs		surfactant protein C																																				SO:0001631	upstream_gene_variant	6440				respiratory gaseous exchange	extracellular space		g.chr8:22021060_22021061delGT		CCDS6026.1, CCDS34856.1	8p21	2013-02-06	2004-08-09		ENSG00000168487	ENSG00000168487	3.4.24.19	"""Bone morphogenetic proteins"""	1067	protein-coding gene	gene with protein product	"""procollagen C-endopeptidase"""	112264	"""procollagen C-endopeptidase"""	PCOLC		2004778	Standard	NM_006129		Approved		uc003xbg.3	P13497	OTTHUMG00000097761		8.37:g.22021070_22021071delGT	Exception_encountered					SFTPC_ENST00000520605.1_Splice_Site|SFTPC_ENST00000437090.2_Splice_Site|SFTPC_ENST00000524255.1_Splice_Site|SFTPC_ENST00000318561.3_Splice_Site|SFTPC_ENST00000521315.1_Splice_Site	p.V146fs			P11686	PSPC_HUMAN		Colorectal(74;0.00191)|COAD - Colon adenocarcinoma(73;0.0615)|READ - Rectum adenocarcinoma(644;0.1)	4	460_461	+			146			BRICHOS.		A8K6F5|B2RN46|D3DSR0|Q13292|Q13872|Q14874|Q99421|Q99422|Q99423|Q9UL38	Frame_Shift_Del	DEL	ENST00000306385.5	37	c.436_437delGT	CCDS6026.1																																																																																				0.545	BMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214995.2	NM_006132		7	154						7	154	---	---	---	---
WHSC1L1	54904	broad.mit.edu	37	8	38205092	38205092	+	Frame_Shift_Del	DEL	T	T	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr8:38205092delT	ENST00000317025.8	-	2	1115	c.598delA	c.(598-600)agcfs	p.S200fs	WHSC1L1_ENST00000527502.1_Frame_Shift_Del_p.S200fs|WHSC1L1_ENST00000316985.3_Frame_Shift_Del_p.S200fs|WHSC1L1_ENST00000433384.2_Frame_Shift_Del_p.S200fs	NM_023034.1	NP_075447.1	Q9BZ95	NSD3_HUMAN	Wolf-Hirschhorn syndrome candidate 1-like 1	200					histone lysine methylation (GO:0034968)|histone methylation (GO:0016571)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	24	Colorectal(12;0.000442)|Esophageal squamous(3;0.0725)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065)	Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511)			TGCTTGTTGCTTTTTTTCCTC	0.378			T	NUP98	AML																																	ENST00000317025.8				Dom	yes		8	8p12	54904	T	Wolf-Hirschhorn syndrome candidate 1-like 1 (NSD3)			L	NUP98		AML		0				NS(1)|breast(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	24						c.(598-600)gcfs		Wolf-Hirschhorn syndrome candidate 1-like 1							203.0	182.0	189.0					8																	38205092		2203	4300	6503	SO:0001589	frameshift_variant	54904				cell differentiation|cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome	histone-lysine N-methyltransferase activity|zinc ion binding	g.chr8:38205092delT	AF332469	CCDS6105.1, CCDS43729.1	8p11.2	2013-05-20			ENSG00000147548	ENSG00000147548			12767	protein-coding gene	gene with protein product		607083				10802047, 23269674	Standard	NM_023034		Approved	FLJ20353, NSD3	uc003xli.3	Q9BZ95		ENST00000317025.8:c.598delA	8.37:g.38205092delT	ENSP00000313983:p.Ser200fs					WHSC1L1_ENST00000316985.3_Frame_Shift_Del_p.S200fs|WHSC1L1_ENST00000433384.2_Frame_Shift_Del_p.S200fs|WHSC1L1_ENST00000527502.1_Frame_Shift_Del_p.S200fs	p.S200fs	NM_023034.1	NP_075447.1	Q9BZ95	NSD3_HUMAN	Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511)		2	1115	-	Colorectal(12;0.000442)|Esophageal squamous(3;0.0725)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065)	200					B7ZL11|D3DSX1|Q1RMD3|Q3B796|Q6ZSA5|Q9BYU8|Q9BYU9|Q9H2M8|Q9H9W9|Q9NXA6	Frame_Shift_Del	DEL	ENST00000317025.8	37	c.598delA	CCDS43729.1																																																																																				0.378	WHSC1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381924.3	NM_023034		7	833						7	833	---	---	---	---
RP11-586K2.1	0	broad.mit.edu	37	8	89498121	89498122	+	RNA	INS	-	-	A			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr8:89498121_89498122insA	ENST00000521433.1	+	0	179				RP11-586K2.1_ENST00000523254.1_RNA																							gaacagctatgaaaaaaaaaac	0.386																																						ENST00000521433.1																			0																																																			0							g.chr8:89498121_89498122insA																													8.37:g.89498131_89498131dupA						RP11-586K2.1_ENST00000523254.1_RNA								0	179	+									RNA	INS	ENST00000521433.1	37																																																																																						0.386	RP11-586K2.1-001	KNOWN	basic	antisense	antisense	OTTHUMT00000375309.2			7	79						7	79	---	---	---	---
ANKRD20A1	84210	broad.mit.edu	37	9	67934791	67934794	+	Frame_Shift_Del	DEL	AAAG	AAAG	-	rs375030402|rs550666541	byFrequency	TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr9:67934791_67934794delAAAG	ENST00000377477.2	+	4	673_676	c.561_564delAAAG	c.(559-564)aaaaagfs	p.KK187fs	RNU6-368P_ENST00000391117.1_RNA	NM_032250.3	NP_115626.2	Q5TYW2	A20A1_HUMAN	ankyrin repeat domain 20 family, member A1	187						plasma membrane (GO:0005886)				kidney(1)|large_intestine(4)|lung(5)|urinary_tract(1)	11						TTTTATTGAAAAAGAAAGCAAGTT	0.309														73	0.0145767	0.0	0.0086	5008	,	,		20736	0.003		0.0239	False		,,,				2504	0.0409					ENST00000377477.2																			0				kidney(1)|large_intestine(4)|lung(5)|urinary_tract(1)	11						c.(559-564)aafs		ankyrin repeat domain 20 family, member A1																																				SO:0001589	frameshift_variant	84210							g.chr9:67934791_67934794delAAAG	AL136793	CCDS6620.1	9p12	2014-04-16	2005-08-23	2005-08-23	ENSG00000196774	ENSG00000260691		"""Ankyrin repeat domain containing"""	23665	protein-coding gene	gene with protein product			"""ankyrin repeat domain 20A"""	ANKRD20A			Standard	NM_032250		Approved	DKFZp434A171		Q5TYW2	OTTHUMG00000188594	ENST00000377477.2:c.561_564delAAAG	9.37:g.67934795_67934798delAAAG	ENSP00000366697:p.Lys187fs						p.KK187fs	NM_032250.3	NP_115626.2					4	673_676	+								Q9H0H6	Frame_Shift_Del	DEL	ENST00000377477.2	37	c.561_564delAAAG	CCDS6620.1																																																																																				0.309	ANKRD20A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083800.1			10	40						10	40	---	---	---	---
ROR2	4920	broad.mit.edu	37	9	94486026	94486028	+	In_Frame_Del	DEL	TCC	TCC	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr9:94486026_94486028delTCC	ENST00000375708.3	-	9	2946_2948	c.2748_2750delGGA	c.(2746-2751)gaggaa>gaa	p.916_917EE>E	ROR2_ENST00000550066.1_5'UTR|ROR2_ENST00000375715.1_Intron	NM_004560.3	NP_004551.2	Q01974	ROR2_HUMAN	receptor tyrosine kinase-like orphan receptor 2	916					cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|embryonic genitalia morphogenesis (GO:0030538)|inner ear morphogenesis (GO:0042472)|JNK cascade (GO:0007254)|multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)|somitogenesis (GO:0001756)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	clathrin-coated endocytic vesicle membrane (GO:0030669)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|Wnt-protein binding (GO:0017147)			autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(31)|ovary(3)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						GACAGAGCCTTCCTCCTCCTCCT	0.645																																						ENST00000375708.3																			0				autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(31)|ovary(3)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						c.(2746-2751)gaa>ga		receptor tyrosine kinase-like orphan receptor 2																																				SO:0001651	inframe_deletion	4920				negative regulation of cell proliferation|positive regulation of cell migration|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity|Wnt-protein binding	g.chr9:94486026_94486028delTCC	M97639	CCDS6691.1	9q22	2013-01-11			ENSG00000169071	ENSG00000169071		"""Immunoglobulin superfamily / I-set domain containing"""	10257	protein-coding gene	gene with protein product		602337		NTRKR2, BDB, BDB1		1334494, 10700182	Standard	NM_004560		Approved		uc004arj.2	Q01974	OTTHUMG00000020211	ENST00000375708.3:c.2748_2750delGGA	9.37:g.94486035_94486037delTCC	ENSP00000364860:p.Glu917del					ROR2_ENST00000375715.1_Intron|ROR2_ENST00000550066.1_5'UTR	p.EE916del	NM_004560.3	NP_004551.2	Q01974	ROR2_HUMAN			9	2946_2948	-			916					Q59GF5|Q5SPI5|Q9HAY7|Q9HB61	In_Frame_Del	DEL	ENST00000375708.3	37	c.2748_2750delGGA	CCDS6691.1																																																																																				0.645	ROR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053040.1			10	638						10	638	---	---	---	---
LINC00475	158314	broad.mit.edu	37	9	94904432	94904432	+	RNA	DEL	G	G	-	rs34310564	byFrequency	TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr9:94904432delG	ENST00000416438.2	+	0	184				snoU13_ENST00000459125.1_RNA	NR_027341.1				long intergenic non-protein coding RNA 475																		GGCCTTCTTTGGGGGGGGGGT	0.612													|||unknown(HR)	1764	0.352236	0.3396	0.4957	5008	,	,		14095	0.371		0.2286	False		,,,				2504	0.3753					ENST00000416438.2																			0																																																			0							g.chr9:94904432delG	AK023662		9q22.31	2012-10-12	2011-08-31	2011-08-31	ENSG00000225511	ENSG00000225511		"""Long non-coding RNAs"""	23569	non-coding RNA	RNA, long non-coding			"""chromosome 9 open reading frame 44"""	C9orf44			Standard	NR_027341		Approved		uc004arp.1		OTTHUMG00000020216		9.37:g.94904432delG								NR_027341.1						0	184	+									RNA	DEL	ENST00000416438.2	37																																																																																						0.612	LINC00475-003	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000053051.2			14	5						14	5	---	---	---	---
MPP7	143098	broad.mit.edu	37	10	28378639	28378649	+	Frame_Shift_Del	DEL	GCCGATACGGT	GCCGATACGGT	-	rs141204011|rs148352336		TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr10:28378639_28378649delGCCGATACGGT	ENST00000375732.1	-	12	1333_1343	c.1074_1084delACCGTATCGGC	c.(1072-1086)acaccgtatcggcgafs	p.PYRR359fs	MPP7_ENST00000540098.1_Frame_Shift_Del_p.PYRR359fs|MPP7_ENST00000375719.3_Frame_Shift_Del_p.PYRR359fs|MPP7_ENST00000337532.5_Frame_Shift_Del_p.PYRR359fs|MPP7_ENST00000445954.2_Frame_Shift_Del_p.PYRR234fs			Q5T2T1	MPP7_HUMAN	membrane protein, palmitoylated 7 (MAGUK p55 subfamily member 7)	359					establishment of cell polarity (GO:0030010)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of signal transduction (GO:0009967)|protein localization to adherens junction (GO:0071896)|tight junction assembly (GO:0070830)	adherens junction (GO:0005912)|cell junction (GO:0030054)|mitochondrion (GO:0005739)|MPP7-DLG1-LIN7 complex (GO:0097025)|tight junction (GO:0005923)	protein complex scaffold (GO:0032947)|protein domain specific binding (GO:0019904)|protein heterodimerization activity (GO:0046982)|signaling adaptor activity (GO:0035591)	p.R361Q(1)|p.P359P(1)		autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|skin(1)|stomach(1)	22						TTAGTTTGTCGCCGATACGGTGTCACTTCTT	0.384																																						ENST00000337532.5																			2	Substitution - Missense(1)|Substitution - coding silent(1)	p.R361Q(1)|p.P359P(1)	lung(1)|endometrium(1)	autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|skin(1)|stomach(1)	22						c.(1072-1086)acgafs		membrane protein, palmitoylated 7 (MAGUK p55 subfamily member 7)																																				SO:0001589	frameshift_variant	143098				establishment of cell polarity|positive regulation of protein complex assembly|protein localization to adherens junction|tight junction assembly	MPP7-DLG1-LIN7 complex|tight junction	protein complex scaffold|protein domain specific binding|protein heterodimerization activity|signaling adaptor activity	g.chr10:28378639_28378649delGCCGATACGGT	BC038105	CCDS7158.1	10p12.1	2004-01-15			ENSG00000150054	ENSG00000150054			26542	protein-coding gene	gene with protein product		610973				14719143	Standard	NM_173496		Approved	FLJ32798	uc001iua.1	Q5T2T1	OTTHUMG00000017868	ENST00000375732.1:c.1074_1084delACCGTATCGGC	10.37:g.28378639_28378649delGCCGATACGGT	ENSP00000364884:p.Pro359fs					MPP7_ENST00000375732.1_Frame_Shift_Del_p.TPYRR358fs|MPP7_ENST00000540098.1_Frame_Shift_Del_p.TPYRR358fs|MPP7_ENST00000445954.2_Frame_Shift_Del_p.TPYRR233fs|MPP7_ENST00000375719.3_Frame_Shift_Del_p.TPYRR358fs	p.TPYRR358fs	NM_173496.3	NP_775767.2	Q5T2T1	MPP7_HUMAN			13	1350_1360	-			358					B2RCC9|B4DWL9|B5MDZ3|D3DRW3|Q5T2T0|Q8IY28	Frame_Shift_Del	DEL	ENST00000375732.1	37	c.1074_1084delACCGTATCGGC	CCDS7158.1																																																																																				0.384	MPP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047345.1	NM_173496		8	973						8	973	---	---	---	---
PCDH15	65217	broad.mit.edu	37	10	55587198	55587200	+	In_Frame_Del	DEL	GGC	GGC	-	rs12246234		TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr10:55587198_55587200delGGC	ENST00000320301.6	-	32	4714_4716	c.4320_4322delGCC	c.(4318-4323)ccgcct>cct	p.1440_1441PP>P	PCDH15_ENST00000414778.1_In_Frame_Del_p.1442_1443PP>P|PCDH15_ENST00000373965.2_In_Frame_Del_p.1447_1448PP>P|PCDH15_ENST00000395446.1_Intron|PCDH15_ENST00000361849.3_In_Frame_Del_p.1440_1441PP>P|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000395445.1_In_Frame_Del_p.1447_1448PP>P|PCDH15_ENST00000437009.1_In_Frame_Del_p.1369_1370PP>P|PCDH15_ENST00000395432.2_In_Frame_Del_p.1400_1401PP>P|PCDH15_ENST00000395433.1_In_Frame_Del_p.1415_1416PP>P|PCDH15_ENST00000463095.1_5'UTR|PCDH15_ENST00000395430.1_In_Frame_Del_p.1437_1438PP>P|PCDH15_ENST00000395438.1_In_Frame_Del_p.1440_1441PP>P|PCDH15_ENST00000409834.1_In_Frame_Del_p.1051_1052PP>P|PCDH15_ENST00000373957.3_Intron	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	1440	Poly-Pro.				equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				ACCTggcggaggcggcggcggcg	0.571										HNSCC(58;0.16)																												ENST00000373965.2																			0				NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237						c.(4339-4344)cct>cc		protocadherin-related 15																																				SO:0001651	inframe_deletion	65217				equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound	extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse	calcium ion binding	g.chr10:55587198_55587200delGGC	AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"""Cadherins / Cadherin-related"""	14674	protein-coding gene	gene with protein product	"""cadherin-related family member 15"""	605514	"""deafness, autosomal recessive 23"", ""protocadherin 15"""	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.4320_4322delGCC	10.37:g.55587207_55587209delGGC	ENSP00000322604:p.Pro1443del	HNSCC(58;0.16)				PCDH15_ENST00000414778.1_In_Frame_Del_p.PP1444del|PCDH15_ENST00000395430.1_In_Frame_Del_p.PP1439del|PCDH15_ENST00000395433.1_In_Frame_Del_p.PP1417del|PCDH15_ENST00000373957.3_Intron|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000395445.1_In_Frame_Del_p.PP1449del|PCDH15_ENST00000409834.1_In_Frame_Del_p.PP1053del|PCDH15_ENST00000395438.1_In_Frame_Del_p.PP1442del|PCDH15_ENST00000437009.1_In_Frame_Del_p.PP1371del|PCDH15_ENST00000463095.1_5'UTR|PCDH15_ENST00000395432.2_In_Frame_Del_p.PP1402del|PCDH15_ENST00000395446.1_Intron|PCDH15_ENST00000320301.6_In_Frame_Del_p.PP1442del|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000361849.3_In_Frame_Del_p.PP1442del	p.PP1449del	NM_001142771.1|NM_001142772.1	NP_001136243.1|NP_001136244.1	Q96QU1	PCD15_HUMAN			33	4735_4737	-		Melanoma(3;0.117)|Lung SC(717;0.238)	1442					A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	In_Frame_Del	DEL	ENST00000320301.6	37	c.4341_4343delGCC	CCDS7248.1																																																																																				0.571	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056		10	550						10	550	---	---	---	---
ANK3	288	broad.mit.edu	37	10	61828727	61828729	+	In_Frame_Del	DEL	GTG	GTG	-	rs368539157		TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr10:61828727_61828729delGTG	ENST00000280772.2	-	37	12101_12103	c.11910_11912delCAC	c.(11908-11913)accact>act	p.3970_3971TT>T	ANK3_ENST00000355288.2_Intron|ANK3_ENST00000373827.2_Intron|ANK3_ENST00000503366.1_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	3970	Thr-rich.				axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						agtggtggtagtggtggtggtgg	0.468																																						ENST00000280772.1																			0				NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						c.(11908-11913)act>ac		ankyrin 3, node of Ranvier (ankyrin G)																																				SO:0001651	inframe_deletion	288				establishment of protein localization|signal transduction	basolateral plasma membrane|cytoplasm|cytoskeleton	protein binding	g.chr10:61828727_61828729delGTG	U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"""Ankyrin repeat domain containing"""	494	protein-coding gene	gene with protein product	"""ankyrin-3, node of Ranvier"", ""ankyrin-G"""	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.11910_11912delCAC	10.37:g.61828736_61828738delGTG	ENSP00000280772:p.Thr3978del					ANK3_ENST00000355288.2_Intron|ANK3_ENST00000503366.1_Intron|ANK3_ENST00000373827.2_Intron	p.TT3976del	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN			37	12101_12103	-			3976			Thr-rich.		B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	In_Frame_Del	DEL	ENST00000280772.2	37	c.11910_11912delCAC	CCDS7258.1																																																																																				0.468	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		7	766						7	766	---	---	---	---
SYNPO2L	79933	broad.mit.edu	37	10	75406948	75406948	+	Frame_Shift_Del	DEL	A	A	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr10:75406948delA	ENST00000394810.2	-	4	2611	c.2462delT	c.(2461-2463)ttcfs	p.F821fs	SYNPO2L_ENST00000372873.4_Frame_Shift_Del_p.F597fs	NM_001114133.1	NP_001107605.1	Q9H987	SYP2L_HUMAN	synaptopodin 2-like	821	Pro-rich.					cytoskeleton (GO:0005856)|nucleus (GO:0005634)|Z disc (GO:0030018)				breast(2)|endometrium(3)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	Prostate(51;0.0112)					CGCCTGGGGGAAAAAGGGAGA	0.592																																						ENST00000394810.2																			0				breast(2)|endometrium(3)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						c.(2461-2463)tcfs		synaptopodin 2-like							59.0	71.0	67.0					10																	75406948		2201	4300	6501	SO:0001589	frameshift_variant	79933					cytoplasm|cytoskeleton	actin binding	g.chr10:75406948delA	AK022983	CCDS7331.1, CCDS44438.1	10q22.3	2007-12-19			ENSG00000166317	ENSG00000166317			23532	protein-coding gene	gene with protein product							Standard	XM_005270158		Approved	FLJ12921	uc001jut.4	Q9H987	OTTHUMG00000018471	ENST00000394810.2:c.2462delT	10.37:g.75406948delA	ENSP00000378289:p.Phe821fs					SYNPO2L_ENST00000372872.4_Intron|SYNPO2L_ENST00000372873.4_Frame_Shift_Del_p.F597fs	p.F821fs	NM_001114133.1	NP_001107605.1	Q9H987	SYP2L_HUMAN			4	2611	-	Prostate(51;0.0112)		821			Pro-rich.		A5PKV9|Q68A20	Frame_Shift_Del	DEL	ENST00000394810.2	37	c.2462delT	CCDS44438.1																																																																																				0.592	SYNPO2L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316562.2	NM_024875		13	863						13	863	---	---	---	---
ZMIZ1	57178	broad.mit.edu	37	10	81070787	81070789	+	In_Frame_Del	DEL	CTC	CTC	-	rs201441910		TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr10:81070787_81070789delCTC	ENST00000334512.5	+	24	3514_3516	c.2942_2944delCTC	c.(2941-2946)gctcct>gct	p.P986del	ZMIZ1_ENST00000446377.2_Intron	NM_020338.3	NP_065071.1	Q9ULJ6	ZMIZ1_HUMAN	zinc finger, MIZ-type containing 1	986	Pro-rich.				artery morphogenesis (GO:0048844)|cell aging (GO:0007569)|developmental growth (GO:0048589)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)|vitellogenesis (GO:0007296)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(2)|prostate(3)|skin(1)	30	all_cancers(46;0.0292)|Breast(12;8.52e-05)|all_epithelial(25;0.000854)|Prostate(51;0.00985)		Epithelial(14;0.00256)|all cancers(16;0.00726)|Colorectal(32;0.229)			CACAGTGGGGCTCCTCCTCCTCC	0.635																																						ENST00000334512.5																			0				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(2)|prostate(3)|skin(1)	30						c.(2941-2946)gct>g		zinc finger, MIZ-type containing 1				27,4237		10,7,2115						4.7	1.0			109	38,8216		16,6,4105	no	coding	ZMIZ1	NM_020338.3		26,13,6220	A1A1,A1R,RR		0.4604,0.6332,0.5193				65,12453				SO:0001651	inframe_deletion	57178				transcription, DNA-dependent	cytoplasm|nuclear speck	zinc ion binding	g.chr10:81070787_81070789delCTC	AB033050	CCDS7357.1	10q22.3	2012-11-30	2006-10-24	2006-10-24	ENSG00000108175	ENSG00000108175		"""Zinc fingers, MIZ-type"""	16493	protein-coding gene	gene with protein product		607159	"""retinoic acid induced 17"""	RAI17		15626329	Standard	NM_020338		Approved	RP11-519K18.1, KIAA1224, FLJ13541, hZIMP10, Zimp10, MIZ	uc001kaf.2	Q9ULJ6	OTTHUMG00000018560	ENST00000334512.5:c.2942_2944delCTC	10.37:g.81070796_81070798delCTC	ENSP00000334474:p.Pro986del					ZMIZ1_ENST00000446377.2_Intron	p.AP981del	NM_020338.3	NP_065071.1	Q9ULJ6	ZMIZ1_HUMAN	Epithelial(14;0.00256)|all cancers(16;0.00726)|Colorectal(32;0.229)		24	3514_3516	+	all_cancers(46;0.0292)|Breast(12;8.52e-05)|all_epithelial(25;0.000854)|Prostate(51;0.00985)		981			Pro-rich.		Q5JSH9|Q7Z7E6	In_Frame_Del	DEL	ENST00000334512.5	37	c.2942_2944delCTC	CCDS7357.1																																																																																				0.635	ZMIZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048944.2	NM_020338		12	921						12	921	---	---	---	---
TM9SF3	56889	broad.mit.edu	37	10	98336475	98336475	+	Frame_Shift_Del	DEL	T	T	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr10:98336475delT	ENST00000371142.4	-	2	430	c.214delA	c.(214-216)agtfs	p.S72fs		NM_020123.3	NP_064508.3	Q9HD45	TM9S3_HUMAN	transmembrane 9 superfamily member 3	72						integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|kidney(3)|large_intestine(6)|lung(2)|prostate(1)	15		Colorectal(252;0.158)		Epithelial(162;1.84e-09)|all cancers(201;2.84e-08)		TGACTGATACTTTTTTTTGAC	0.363																																						ENST00000371142.4																			0				breast(2)|endometrium(1)|kidney(3)|large_intestine(6)|lung(2)|prostate(1)	15						c.(214-216)gtfs		transmembrane 9 superfamily member 3							146.0	145.0	145.0					10																	98336475		2203	4300	6503	SO:0001589	frameshift_variant	56889					integral to membrane	binding	g.chr10:98336475delT	AF160213, AF269150	CCDS7450.1	10q24.2	2006-04-12			ENSG00000077147	ENSG00000077147			21529	protein-coding gene	gene with protein product						11530251, 11595169	Standard	NM_020123		Approved	SMBP	uc001kmm.4	Q9HD45	OTTHUMG00000018834	ENST00000371142.4:c.214delA	10.37:g.98336475delT	ENSP00000360184:p.Ser72fs						p.S72fs	NM_020123.3	NP_064508.3	Q9HD45	TM9S3_HUMAN		Epithelial(162;1.84e-09)|all cancers(201;2.84e-08)	2	430	-		Colorectal(252;0.158)	72					Q5TB57|Q6UWE7|Q9NWL8|Q9P0G9|Q9UHW8	Frame_Shift_Del	DEL	ENST00000371142.4	37	c.214delA	CCDS7450.1																																																																																				0.363	TM9SF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049610.2	NM_020123		9	761						9	761	---	---	---	---
LZTS2	84445	broad.mit.edu	37	10	102763415	102763417	+	In_Frame_Del	DEL	CCT	CCT	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr10:102763415_102763417delCCT	ENST00000370220.1	+	2	3623_3625	c.560_562delCCT	c.(559-564)gcctcc>gcc	p.S197del	LZTS2_ENST00000370223.3_In_Frame_Del_p.S197del					leucine zipper, putative tumor suppressor 2											breast(1)|large_intestine(6)|lung(7)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	22				Epithelial(162;7.3e-09)|all cancers(201;3.72e-07)		GGGGGCCCTGcctcctcctcctc	0.65																																					Esophageal Squamous(8;38 437 13604 19902 37640)	ENST00000370220.1																			0				breast(1)|large_intestine(6)|lung(7)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	22						c.(559-564)gcc>g		leucine zipper, putative tumor suppressor 2				12,4252		3,6,2123						5.3	1.0			94	17,8235		4,9,4113	no	coding	LZTS2	NM_032429.2		7,15,6236	A1A1,A1R,RR		0.206,0.2814,0.2317				29,12487				SO:0001651	inframe_deletion	84445				cell division|mitosis|Wnt receptor signaling pathway	membrane|microtubule|microtubule organizing center		g.chr10:102763415_102763417delCCT	AB058716	CCDS7507.1	10q24	2004-03-18			ENSG00000107816	ENSG00000107816			29381	protein-coding gene	gene with protein product		610454				11347906, 11709705	Standard	NM_032429		Approved	KIAA1813, LAPSER1	uc001ksj.3	Q9BRK4	OTTHUMG00000018914	ENST00000370220.1:c.560_562delCCT	10.37:g.102763424_102763426delCCT	ENSP00000359240:p.Ser197del					LZTS2_ENST00000370223.3_In_Frame_Del_p.AS187del	p.AS187del			Q9BRK4	LZTS2_HUMAN		Epithelial(162;7.3e-09)|all cancers(201;3.72e-07)	2	3623_3625	+			187			Required for centrosomal localization (By similarity).			In_Frame_Del	DEL	ENST00000370220.1	37	c.560_562delCCT	CCDS7507.1																																																																																				0.650	LZTS2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049872.1	XM_046743		9	1271						9	1271	---	---	---	---
INA	9118	broad.mit.edu	37	10	105048271	105048273	+	In_Frame_Del	DEL	GAG	GAG	-	rs545805667	byFrequency	TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr10:105048271_105048273delGAG	ENST00000369849.4	+	3	1394_1396	c.1345_1347delGAG	c.(1345-1347)gagdel	p.E454del		NM_032727.3	NP_116116.1	Q16352	AINX_HUMAN	internexin neuronal intermediate filament protein, alpha	454	Poly-Glu.|Tail.				cell differentiation (GO:0030154)|neurofilament cytoskeleton organization (GO:0060052)|substantia nigra development (GO:0021762)	cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular space (GO:0005615)|neurofilament (GO:0005883)	structural constituent of cytoskeleton (GO:0005200)	p.E449_E450delEE(1)		breast(2)|endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|prostate(2)	13				Epithelial(162;3.45e-09)|all cancers(201;9.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.198)		ACTTAAGAAAGAGGAGGAGGAGG	0.458														3	0.000599042	0.0008	0.0	5008	,	,		16930	0.001		0.0	False		,,,				2504	0.001					ENST00000369849.4																			1	Deletion - In frame(1)	p.E449_E450delEE(1)	breast(1)	breast(2)|endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|prostate(2)	13						c.(1345-1347)del		internexin neuronal intermediate filament protein, alpha																																				SO:0001651	inframe_deletion	9118				cell differentiation|nervous system development	neurofilament	structural constituent of cytoskeleton	g.chr10:105048271_105048273delGAG	S78296	CCDS7545.1	10q24	2013-01-16			ENSG00000148798	ENSG00000148798		"""Intermediate filaments type IV"""	6057	protein-coding gene	gene with protein product		605338		NEF5		7769995	Standard	NM_032727		Approved	NF-66	uc001kws.3	Q16352	OTTHUMG00000018986	ENST00000369849.4:c.1345_1347delGAG	10.37:g.105048280_105048282delGAG	ENSP00000358865:p.Glu454del						p.E454del	NM_032727.3	NP_116116.1	Q16352	AINX_HUMAN		Epithelial(162;3.45e-09)|all cancers(201;9.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.198)	3	1394_1396	+			454			Poly-Glu.|Tail.		B1AQK0|Q9BRC5	In_Frame_Del	DEL	ENST00000369849.4	37	c.1345_1347delGAG	CCDS7545.1																																																																																				0.458	INA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050145.1	NM_032727		21	594						21	594	---	---	---	---
NUP98	4928	broad.mit.edu	37	11	3720389	3720389	+	Frame_Shift_Del	DEL	T	T	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr11:3720389delT	ENST00000324932.7	-	25	4352	c.3932delA	c.(3931-3933)aacfs	p.N1311fs	NUP98_ENST00000359171.4_Frame_Shift_Del_p.N1311fs|NUP98_ENST00000355260.3_Frame_Shift_Del_p.N1311fs|NUP98_ENST00000488828.1_5'Flank	NM_016320.4|NM_139132.3	NP_057404.2|NP_624358.2	P52948	NUP98_HUMAN	nucleoporin 98kDa	1328					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|DNA replication (GO:0006260)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nuclear pore organization (GO:0006999)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nuclear pore outer ring (GO:0031080)|nucleoplasm (GO:0005654)	peptide binding (GO:0042277)|structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199)		CACAGGGCTGTTTTTTTGGGT	0.512			T	"""HOXA9, NSD1, WHSC1L1, DDX10, TOP1, HOXD13, PMX1, HOXA13, HOXD11, HOXA11, RAP1GDS1, HOXC11"""	AML																																	ENST00000324932.7				Dom	yes		11	11p15	4928	T	nucleoporin 98kDa			L	"""HOXA9, NSD1, WHSC1L1, DDX10, TOP1, HOXD13, PMX1, HOXA13, HOXD11, HOXA11, RAP1GDS1, HOXC11"""		AML		0				NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66						c.(3931-3933)acfs		nucleoporin 98kDa							176.0	183.0	180.0					11																	3720389		2201	4298	6499	SO:0001589	frameshift_variant	4928				carbohydrate metabolic process|DNA replication|glucose transport|interspecies interaction between organisms|mitotic prometaphase|mRNA transport|nuclear pore organization|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear membrane|nucleoplasm|Nup107-160 complex	protein binding|structural constituent of nuclear pore|transporter activity	g.chr11:3720389delT	AF071076, AF231130, BC012906, BG773331	CCDS7746.1, CCDS31347.1, CCDS41605.1, CCDS41606.1	11p15	2008-02-26	2002-08-29		ENSG00000110713	ENSG00000110713			8068	protein-coding gene	gene with protein product		601021	"""nucleoporin 98kD"""			9166830	Standard	NM_139131		Approved	NUP96	uc001lyh.3	P52948	OTTHUMG00000011846	ENST00000324932.7:c.3932delA	11.37:g.3720389delT	ENSP00000316032:p.Asn1311fs					NUP98_ENST00000355260.3_Frame_Shift_Del_p.N1311fs|NUP98_ENST00000359171.4_Frame_Shift_Del_p.N1311fs	p.N1311fs	NM_016320.4|NM_139132.3	NP_057404.2|NP_624358.2	P52948	NUP98_HUMAN		BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199)	25	4352	-		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)	1328					Q8IUT2|Q8WYB0|Q96E54|Q9H3Q4|Q9NT02|Q9UF57|Q9UHX0|Q9Y6J4|Q9Y6J5	Frame_Shift_Del	DEL	ENST00000324932.7	37	c.3932delA	CCDS7746.1																																																																																				0.512	NUP98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032766.3	NM_016320		7	1382						7	1382	---	---	---	---
OR10A2	341276	broad.mit.edu	37	11	6891253	6891255	+	In_Frame_Del	DEL	TTC	TTC	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr11:6891253_6891255delTTC	ENST00000307322.4	+	1	330_332	c.268_270delTTC	c.(268-270)ttcdel	p.F94del		NM_001004460.1	NP_001004460.1	Q9H208	O10A2_HUMAN	olfactory receptor, family 10, subfamily A, member 2	94						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(12)|urinary_tract(1)	24		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.89e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		TCAGATGTATTTCTTCTTCTTCT	0.517																																						ENST00000307322.4																			0				NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(12)|urinary_tract(1)	24						c.(268-270)del		olfactory receptor, family 10, subfamily A, member 2																																				SO:0001651	inframe_deletion	341276				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr11:6891253_6891255delTTC	BK004293	CCDS31415.1	11p15.4	2012-08-09		2004-03-10	ENSG00000170790	ENSG00000170790		"""GPCR / Class A : Olfactory receptors"""	8161	protein-coding gene	gene with protein product				OR10A2P			Standard	NM_001004460		Approved	OST363	uc001meu.1	Q9H208	OTTHUMG00000165739	ENST00000307322.4:c.268_270delTTC	11.37:g.6891262_6891264delTTC	ENSP00000303862:p.Phe94del						p.F94del	NM_001004460.1	NP_001004460.1	Q9H208	O10A2_HUMAN		Epithelial(150;4.89e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)	1	330_332	+		Medulloblastoma(188;0.0523)|all_neural(188;0.236)	94					B2RNL9|Q6IFG9	In_Frame_Del	DEL	ENST00000307322.4	37	c.268_270delTTC	CCDS31415.1																																																																																				0.517	OR10A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385984.1	NM_001004460		8	871						8	871	---	---	---	---
PLEKHA7	144100	broad.mit.edu	37	11	16822525	16822525	+	Frame_Shift_Del	DEL	A	A	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr11:16822525delA	ENST00000355661.3	-	17	2415	c.2405delT	c.(2404-2406)ttcfs	p.F802fs	PLEKHA7_ENST00000448080.2_Frame_Shift_Del_p.F802fs|PLEKHA7_ENST00000531066.1_Frame_Shift_Del_p.F802fs|PLEKHA7_ENST00000532079.1_Intron			Q6IQ23	PKHA7_HUMAN	pleckstrin homology domain containing, family A member 7	802					epithelial cell-cell adhesion (GO:0090136)|zonula adherens maintenance (GO:0045218)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|zonula adherens (GO:0005915)	delta-catenin binding (GO:0070097)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(13)|ovary(1)|prostate(2)|skin(7)|urinary_tract(1)	37						GGTCACCTGGAAAAAAAAGGC	0.443																																						ENST00000355661.3																			0				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(13)|ovary(1)|prostate(2)|skin(7)|urinary_tract(1)	37						c.(2404-2406)tcfs		pleckstrin homology domain containing, family A member 7							234.0	234.0	234.0					11																	16822525		2200	4294	6494	SO:0001589	frameshift_variant	144100				epithelial cell-cell adhesion|zonula adherens maintenance	centrosome|zonula adherens	delta-catenin binding	g.chr11:16822525delA	BC033239	CCDS31434.1	11p15	2013-01-10			ENSG00000166689	ENSG00000166689		"""Pleckstrin homology (PH) domain containing"""	27049	protein-coding gene	gene with protein product		612686				12477932	Standard	NM_175058		Approved	DKFZp686M22243	uc001mmo.3	Q6IQ23	OTTHUMG00000165954	ENST00000355661.3:c.2405delT	11.37:g.16822525delA	ENSP00000347883:p.Phe802fs					PLEKHA7_ENST00000448080.2_Frame_Shift_Del_p.F802fs|PLEKHA7_ENST00000532079.1_Intron|PLEKHA7_ENST00000531066.1_Frame_Shift_Del_p.F802fs	p.F802fs			Q6IQ23	PKHA7_HUMAN			17	2415	-			802					B4DK33|B4DWC3|Q86VZ7	Frame_Shift_Del	DEL	ENST00000355661.3	37	c.2405delT	CCDS31434.1																																																																																				0.443	PLEKHA7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000387242.2	NM_175058		10	976						10	976	---	---	---	---
NAV2	89797	broad.mit.edu	37	11	19901475	19901477	+	In_Frame_Del	DEL	AGC	AGC	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr11:19901475_19901477delAGC	ENST00000396087.3	+	5	671_673	c.572_574delAGC	c.(571-576)aagcag>aag	p.Q196del	NAV2_ENST00000360655.4_In_Frame_Del_p.Q132del|NAV2_ENST00000396085.1_In_Frame_Del_p.Q196del|NAV2_ENST00000349880.4_In_Frame_Del_p.Q196del|NAV2_ENST00000540292.1_In_Frame_Del_p.Q127del|NAV2_ENST00000527559.2_In_Frame_Del_p.Q125del|NAV2_ENST00000534229.1_3'UTR	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	196	Gln-rich.				glossopharyngeal nerve development (GO:0021563)|locomotory behavior (GO:0007626)|optic nerve development (GO:0021554)|regulation of systemic arterial blood pressure by baroreceptor feedback (GO:0003025)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|vagus nerve development (GO:0021564)	interstitial matrix (GO:0005614)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|heparin binding (GO:0008201)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(26)|lung(38)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	116						TCCCGATACAagcagcagcagca	0.611																																						ENST00000396085.1																			0				NS(1)|breast(2)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(26)|lung(38)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	116						c.(571-576)aag>a		neuron navigator 2			,,	52,4210		4,44,2083					,,	5.9	1.0			68	58,8184		2,54,4065	no	coding,coding,coding	NAV2	NM_182964.5,NM_145117.4,NM_001111018.1	,,	6,98,6148	A1A1,A1R,RR		0.7037,1.2201,0.8797	,,	,,		110,12394				SO:0001651	inframe_deletion	89797					nucleus	ATP binding|helicase activity	g.chr11:19901475_19901477delAGC	AB037840	CCDS7850.1, CCDS7851.2, CCDS44552.1, CCDS53612.1, CCDS58126.1	11p15.1	2008-07-18			ENSG00000166833	ENSG00000166833	3.6.1.1		15997	protein-coding gene	gene with protein product	"""pore membrane and/or filament interacting like protein 2"", ""retinoic acid inducible gene in neuroblastoma 1"", ""helicase, APC down-regulated 1"""	607026				12079279, 12062803	Standard	NM_145117		Approved	FLJ10633, FLJ11030, HELAD1, KIAA1419, POMFIL2, RAINB1, FLJ23707	uc010rdm.2	Q8IVL1	OTTHUMG00000151837	ENST00000396087.3:c.572_574delAGC	11.37:g.19901484_19901486delAGC	ENSP00000379396:p.Gln196del					NAV2_ENST00000534229.1_3'UTR|NAV2_ENST00000540292.1_In_Frame_Del_p.KQ122del|NAV2_ENST00000349880.4_In_Frame_Del_p.KQ191del|NAV2_ENST00000396087.3_In_Frame_Del_p.KQ191del|NAV2_ENST00000527559.2_In_Frame_Del_p.KQ120del|NAV2_ENST00000360655.4_In_Frame_Del_p.KQ127del	p.KQ191del	NM_182964.5	NP_892009.3	Q8IVL1	NAV2_HUMAN			5	933_935	+			191			CH.		A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	In_Frame_Del	DEL	ENST00000396087.3	37	c.572_574delAGC	CCDS58126.1																																																																																				0.611	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117		15	645						15	645	---	---	---	---
MRPL49	740	broad.mit.edu	37	11	64888248	64888250	+	5'Flank	DEL	TCT	TCT	-	rs1065065		TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr11:64888248_64888250delTCT	ENST00000279242.2	+	0	0				FAU_ENST00000527548.1_In_Frame_Del_p.K102del|FAU_ENST00000529639.1_In_Frame_Del_p.K102del|FAU_ENST00000525297.1_In_Frame_Del_p.K67del|MRPL49_ENST00000534078.1_5'Flank|FAU_ENST00000531743.1_In_Frame_Del_p.K102del|FAU_ENST00000279259.3_In_Frame_Del_p.E83del|MRPL49_ENST00000531705.1_5'Flank|MRPL49_ENST00000526171.1_5'Flank|FAU_ENST00000529259.1_3'UTR	NM_004927.3	NP_004918.1	Q13405	RM49_HUMAN	mitochondrial ribosomal protein L49						translation (GO:0006412)	mitochondrial ribosome (GO:0005761)	structural constituent of ribosome (GO:0003735)			endometrium(1)|ovary(1)	2						GCCCGACCTGTCTTCTTCTTCTT	0.542																																						ENST00000529639.1																			0				NS(3)|kidney(1)|large_intestine(2)	6						c.(304-309)aca>a		Finkel-Biskis-Reilly murine sarcoma virus (FBR-MuSV) ubiquitously expressed																																				SO:0001631	upstream_gene_variant	2197							g.chr11:64888248_64888250delTCT		CCDS8096.1	11q13.1	2012-11-14	2001-10-16	2001-10-19	ENSG00000149792	ENSG00000149792		"""Mitochondrial ribosomal proteins / large subunits"""	1176	protein-coding gene	gene with protein product	"""neighbor of FAU"", ""next to FAU"""	606866	"""chromosome 11 open reading frame 4"""	C11orf4		8786148	Standard	NM_004927		Approved	NOF, NOF1, L49mt	uc001oda.2	Q13405	OTTHUMG00000165608		11.37:g.64888257_64888259delTCT	Exception_encountered					FAU_ENST00000531743.1_In_Frame_Del_p.KT102del|FAU_ENST00000525297.1_In_Frame_Del_p.KT67del|FAU_ENST00000529259.1_3'UTR|FAU_ENST00000527548.1_In_Frame_Del_p.KT102del|FAU_ENST00000279259.3_In_Frame_Del_p.ED83del	p.KT102del	NM_001997.4	NP_001988.1	P35544	UBIM_HUMAN			5	696_698	-			0					B2R4G6	In_Frame_Del	DEL	ENST00000279242.2	37	c.305_307delAGA	CCDS8096.1																																																																																				0.542	MRPL49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385293.1	NM_004927		7	832						7	832	---	---	---	---
LRFN4	78999	broad.mit.edu	37	11	66625231	66625233	+	In_Frame_Del	DEL	CTG	CTG	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr11:66625231_66625233delCTG	ENST00000309602.4	+	1	259_261	c.16_18delCTG	c.(16-18)ctgdel	p.L10del	LRFN4_ENST00000393952.3_In_Frame_Del_p.L10del|PC_ENST00000393955.2_Intron|PC_ENST00000393960.1_Intron|PC_ENST00000393958.2_Intron|LRFN4_ENST00000531590.1_3'UTR	NM_024036.4	NP_076941.2	Q6PJG9	LRFN4_HUMAN	leucine rich repeat and fibronectin type III domain containing 4	10						integral component of membrane (GO:0016021)				breast(1)|lung(1)|prostate(1)	3						CCCGCCGCTCCTGCTGCTGCTGC	0.719																																						ENST00000309602.4																			0				breast(1)|lung(1)|prostate(1)	3						c.(16-18)del		leucine rich repeat and fibronectin type III domain containing 4			,,,	48,4006		2,44,1981					,,,	0.9	1.0			14	131,7663		10,111,3776	no	coding,intron,intron,intron	PC,LRFN4	NM_024036.4,NM_022172.2,NM_001040716.1,NM_000920.3	,,,	12,155,5757	A1A1,A1R,RR		1.6808,1.184,1.5108	,,,	,,,		179,11669				SO:0001651	inframe_deletion	78999					integral to membrane		g.chr11:66625231_66625233delCTG	BC007718	CCDS8153.1	11q13.1	2013-02-11				ENSG00000173621		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	28456	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 6"""	612810				16495444, 16828986	Standard	NM_024036		Approved	MGC3103, SALM3., FIGLER6	uc001ojr.3	Q6PJG9		ENST00000309602.4:c.16_18delCTG	11.37:g.66625240_66625242delCTG	ENSP00000312535:p.Leu10del					PC_ENST00000393955.2_Intron|PC_ENST00000393958.2_Intron|PC_ENST00000393960.1_Intron|LRFN4_ENST00000393952.3_In_Frame_Del_p.L10del|LRFN4_ENST00000531590.1_3'UTR	p.L10del	NM_024036.4	NP_076941.2	Q6PJG9	LRFN4_HUMAN			1	259_261	+			10					Q4VBZ3|Q59GV4|Q8N644|Q9BWJ0	In_Frame_Del	DEL	ENST00000309602.4	37	c.16_18delCTG	CCDS8153.1																																																																																				0.719	LRFN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393127.1	NM_024036		7	169						7	169	---	---	---	---
FOLH1B	219595	broad.mit.edu	37	11	89405323	89405326	+	RNA	DEL	TTTA	TTTA	-	rs539338573|rs34562444	byFrequency	TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr11:89405323_89405326delTTTA	ENST00000532352.1	+	0	1114							Q9HBA9	FOH1B_HUMAN	folate hydrolase 1B							cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(26)|ovary(4)|skin(4)|urinary_tract(2)	48						aattatattgtttatttatttttg	0.23														1083	0.216254	0.1286	0.2435	5008	,	,		17643	0.1319		0.3718	False		,,,				2504	0.2423					ENST00000532352.1																			0				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(26)|ovary(4)|skin(4)|urinary_tract(2)	48								folate hydrolase 1B																																						219595				proteolysis	cytoplasm	dipeptidase activity|metal ion binding|metallopeptidase activity	g.chr11:89405323_89405326delTTTA	AF261715		11q14.3	2014-03-18			ENSG00000134612	ENSG00000134612			13636	protein-coding gene	gene with protein product	"""prostate specific membrane antigen like protein"", ""Cell growth-inhibiting gene 26 protein"", ""glutamate carboxypeptidase III"""	609020	"""folate hydrolase 2"""	FOLH2, FOLHP		9838072, 14716746	Standard	NM_153696		Approved	PSMAL, GCPIII	uc001pda.3	Q9HBA9	OTTHUMG00000167376		11.37:g.89405327_89405330delTTTA										Q9HBA9	FOH1B_HUMAN			0	1114	+									RNA	DEL	ENST00000532352.1	37																																																																																						0.230	FOLH1B-004	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000395421.1	NM_153696		12	29						12	29	---	---	---	---
DPAGT1	1798	broad.mit.edu	37	11	118969143	118969143	+	Frame_Shift_Del	DEL	A	A	-	rs35482889		TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr11:118969143delA	ENST00000409993.2	-	7	2249	c.698delT	c.(697-699)ttcfs	p.F233fs	DPAGT1_ENST00000354202.4_Frame_Shift_Del_p.F233fs|DPAGT1_ENST00000432443.2_Frame_Shift_Del_p.F126fs|H2AFX_ENST00000530167.1_5'Flank|DPAGT1_ENST00000445653.1_5'Flank			Q9H3H5	GPT_HUMAN	dolichyl-phosphate (UDP-N-acetylglucosamine) N-acetylglucosaminephosphotransferase 1 (GlcNAc-1-P transferase)	233					cellular protein metabolic process (GO:0044267)|dolichol biosynthetic process (GO:0019408)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)|protein oligomerization (GO:0051259)|UDP-N-acetylglucosamine metabolic process (GO:0006047)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	phospho-N-acetylmuramoyl-pentapeptide-transferase activity (GO:0008963)|transferase activity, transferring glycosyl groups (GO:0016757)|UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase activity (GO:0003975)	p.?(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(2)	17	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.55e-05)		CAAAGTGGTGAAAAAAAAGGG	0.438																																						ENST00000409993.2																			1	Unknown(1)	p.?(1)	skin(1)	breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(2)	17						c.(697-699)tcfs		dolichyl-phosphate (UDP-N-acetylglucosamine) N-acetylglucosaminephosphotransferase 1 (GlcNAc-1-P transferase)							197.0	180.0	186.0					11																	118969143		2200	4295	6495	SO:0001589	frameshift_variant	1798				dolichol biosynthetic process|dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine|protein oligomerization	integral to endoplasmic reticulum membrane|microsome	phospho-N-acetylmuramoyl-pentapeptide-transferase activity|transferase activity, transferring glycosyl groups|UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase activity	g.chr11:118969143delA	Z82022	CCDS8411.1	11q23.3	2007-12-14			ENSG00000172269	ENSG00000172269	2.7.8.15		2995	protein-coding gene	gene with protein product		191350		DPAGT2, DPAGT		8244387	Standard	NM_001382		Approved	GPT, D11S366, DGPT, ALG7, CDG-Ij	uc001pvi.3	Q9H3H5	OTTHUMG00000153533	ENST00000409993.2:c.698delT	11.37:g.118969143delA	ENSP00000386597:p.Phe233fs					DPAGT1_ENST00000432443.2_Frame_Shift_Del_p.F126fs|DPAGT1_ENST00000354202.4_Frame_Shift_Del_p.F233fs	p.F233fs			Q9H3H5	GPT_HUMAN		BRCA - Breast invasive adenocarcinoma(274;7.55e-05)	7	2249	-	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)	233					O15216|Q86WV9|Q9BWE6	Frame_Shift_Del	DEL	ENST00000409993.2	37	c.698delT	CCDS8411.1																																																																																				0.438	DPAGT1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331527.2	NM_001382		7	593						7	593	---	---	---	---
OR8D4	338662	broad.mit.edu	37	11	123777441	123777442	+	Frame_Shift_Ins	INS	-	-	T	rs79561639|rs74740497|rs201238608	byFrequency	TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr11:123777441_123777442insT	ENST00000321355.2	+	1	333_334	c.303_304insT	c.(304-306)tttfs	p.F102fs		NM_001005197.1	NP_001005197.1	Q8NGM9	OR8D4_HUMAN	olfactory receptor, family 8, subfamily D, member 4	102						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(1)|lung(16)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	25		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.93e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0409)		TGATTCAGCTGTTTTTTTTCTG	0.436													TTTTTTTT|TTTTTTTT|TTTTTTTTT|insertion	116	0.0231629	0.084	0.0058	5008	,	,		21496	0.0		0.001	False		,,,				2504	0.0					ENST00000321355.2																			0				large_intestine(1)|lung(16)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	25						c.(301-306)ctttttfs		olfactory receptor, family 8, subfamily D, member 4				222,0,4042		5,0,212,0,0,1915						-6.5	0.6		dbSNP_131	230	2,2,8250		0,0,2,0,2,4123	no	codingComplex	OR8D4	NM_001005197.1		5,0,214,0,2,6038	A1A1,A1A2,A1R,A2A2,A2R,RR		0.0485,5.2064,1.8054				224,2,12292				SO:0001589	frameshift_variant	338662				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr11:123777441_123777442insT	AB065761	CCDS31698.1	11q24.1	2012-08-09			ENSG00000181518	ENSG00000181518		"""GPCR / Class A : Olfactory receptors"""	14840	protein-coding gene	gene with protein product							Standard	NM_001005197		Approved		uc010saa.2	Q8NGM9	OTTHUMG00000165960	ENST00000321355.2:c.311dupT	11.37:g.123777449_123777449dupT	ENSP00000325381:p.Phe102fs						p.LF101fs	NM_001005197.1	NP_001005197.1	Q8NGM9	OR8D4_HUMAN		BRCA - Breast invasive adenocarcinoma(274;4.93e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0409)	1	333_334	+		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)	101					Q6IFE9	Frame_Shift_Ins	INS	ENST00000321355.2	37	c.303_304insT	CCDS31698.1																																																																																				0.436	OR8D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387262.1	NM_001005197		9	1556						9	1556	---	---	---	---
CHD4	1108	broad.mit.edu	37	12	6711207	6711209	+	In_Frame_Del	DEL	CTT	CTT	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr12:6711207_6711209delCTT	ENST00000357008.2	-	4	518_520	c.355_357delAAG	c.(355-357)aagdel	p.K119del	CHD4_ENST00000544040.1_In_Frame_Del_p.K112del|CHD4_ENST00000544484.1_In_Frame_Del_p.K116del|CHD4_ENST00000309577.6_In_Frame_Del_p.K119del	NM_001273.2	NP_001264.2	Q14839	CHD4_HUMAN	chromodomain helicase DNA binding protein 4	119	Poly-Lys.				ATP-dependent chromatin remodeling (GO:0043044)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spindle assembly (GO:0051225)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|RNA polymerase II repressing transcription factor binding (GO:0001103)|zinc ion binding (GO:0008270)	p.K119delK(3)		central_nervous_system(2)	2						TAGGTCCAAGCTTCTTCTTCTTC	0.537																																					Colon(32;586 792 4568 16848 45314)	ENST00000309577.6																			3	Deletion - In frame(3)	p.K119delK(3)	central_nervous_system(3)	central_nervous_system(2)	2						c.(355-357)del		chromodomain helicase DNA binding protein 4				115,4123		4,107,2008						4.7	1.0			29	227,7995		2,223,3886	no	coding	CHD4	NM_001273.2		6,330,5894	A1A1,A1R,RR		2.7609,2.7135,2.7448				342,12118				SO:0001651	inframe_deletion	1108				chromatin modification|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	microtubule organizing center|NuRD complex	ATP binding|ATP-dependent DNA helicase activity|DNA binding|zinc ion binding	g.chr12:6711207_6711209delCTT	X86691	CCDS8552.1	12p13	2013-01-28				ENSG00000111642		"""Zinc fingers, PHD-type"""	1919	protein-coding gene	gene with protein product		603277				7575689, 8843877	Standard	XM_006718958		Approved	Mi-2b, Mi2-BETA	uc001qpo.3	Q14839		ENST00000357008.2:c.355_357delAAG	12.37:g.6711216_6711218delCTT	ENSP00000349508:p.Lys119del					CHD4_ENST00000544040.1_In_Frame_Del_p.K112del|CHD4_ENST00000544484.1_In_Frame_Del_p.K116del|CHD4_ENST00000357008.2_In_Frame_Del_p.K119del	p.K119del			Q14839	CHD4_HUMAN			4	518_520	-			119			Poly-Lys.		Q8IXZ5	In_Frame_Del	DEL	ENST00000357008.2	37	c.355_357delAAG	CCDS8552.1																																																																																				0.537	CHD4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001273		13	319						13	319	---	---	---	---
SLC39A5	283375	broad.mit.edu	37	12	56628997	56628999	+	In_Frame_Del	DEL	CTG	CTG	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr12:56628997_56628999delCTG	ENST00000266980.4	+	5	984_986	c.691_693delCTG	c.(691-693)ctgdel	p.L234del	SLC39A5_ENST00000454355.2_In_Frame_Del_p.L234del|ANKRD52_ENST00000548241.1_5'Flank	NM_001135195.1	NP_001128667.1	Q6ZMH5	S39A5_HUMAN	solute carrier family 39 (zinc transporter), member 5	234					cellular response to zinc ion starvation (GO:0034224)|G1 to G0 transition involved in cell differentiation (GO:0070315)|neural precursor cell proliferation (GO:0061351)|transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	metal ion transmembrane transporter activity (GO:0046873)			NS(1)|cervix(6)|endometrium(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						TCCCCTATCCCTGCTGCTGCTGC	0.635																																						ENST00000266980.4																			0				NS(1)|cervix(6)|endometrium(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						c.(691-693)del		solute carrier family 39 (zinc transporter), member 5																																				SO:0001651	inframe_deletion	283375				zinc ion transport	basolateral plasma membrane|integral to membrane	metal ion transmembrane transporter activity	g.chr12:56628997_56628999delCTG		CCDS8912.2	12q13.3	2013-07-17	2013-07-17		ENSG00000139540	ENSG00000139540		"""Solute carriers"""	20502	protein-coding gene	gene with protein product		608730	"""solute carrier family 39 (metal ion transporter), member 5"""				Standard	NM_173596		Approved		uc010sqj.2	Q6ZMH5	OTTHUMG00000156962	ENST00000266980.4:c.691_693delCTG	12.37:g.56629006_56629008delCTG	ENSP00000266980:p.Leu234del					SLC39A5_ENST00000454355.2_In_Frame_Del_p.L234del	p.L234del	NM_001135195.1	NP_001128667.1	Q6ZMH5	S39A5_HUMAN			5	984_986	+			234					B2R808|Q8N6Y3	In_Frame_Del	DEL	ENST00000266980.4	37	c.691_693delCTG	CCDS8912.2																																																																																				0.635	SLC39A5-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346834.1	NM_173596		7	1352						7	1352	---	---	---	---
UTP20	27340	broad.mit.edu	37	12	101680156	101680157	+	Frame_Shift_Ins	INS	-	-	T			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr12:101680156_101680157insT	ENST00000261637.4	+	5	558_559	c.384_385insT	c.(385-387)tttfs	p.F129fs		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	129					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|negative regulation of cell proliferation (GO:0008285)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|preribosome, small subunit precursor (GO:0030688)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			NS(3)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(26)|lung(30)|ovary(2)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	88						ACTTTCCAGAGTTTTTTTTGAC	0.396																																						ENST00000261637.4																			0				NS(3)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(26)|lung(30)|ovary(2)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	88						c.(382-387)gattttfs		UTP20, small subunit (SSU) processome component, homolog (yeast)																																				SO:0001589	frameshift_variant	27340				endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|negative regulation of cell proliferation	90S preribosome|cytoplasm|nucleolus|nucleoplasm|preribosome, small subunit precursor|small-subunit processome	protein binding	g.chr12:101680156_101680157insT	AJ006778	CCDS9081.1	12q23	2006-02-11				ENSG00000120800			17897	protein-coding gene	gene with protein product	"""down regulated in metastasis"""	612822				9673349, 15590835, 12837249	Standard	NM_014503		Approved	DRIM	uc001tia.1	O75691	OTTHUMG00000170270	ENST00000261637.4:c.392dupT	12.37:g.101680164_101680164dupT	ENSP00000261637:p.Phe129fs						p.DF128fs	NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN			5	558_559	+			128					Q9H3H4	Frame_Shift_Ins	INS	ENST00000261637.4	37	c.384_385insT	CCDS9081.1																																																																																				0.396	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503		10	1401						10	1401	---	---	---	---
CLIP1	6249	broad.mit.edu	37	12	122812690	122812691	+	Frame_Shift_Ins	INS	-	-	T			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr12:122812690_122812691insT	ENST00000540338.1	-	16	3093_3094	c.3052_3053insA	c.(3052-3054)agcfs	p.S1018fs	CLIP1_ENST00000545889.1_Frame_Shift_Ins_p.S593fs|CLIP1_ENST00000361654.4_Frame_Shift_Ins_p.S896fs|CLIP1_ENST00000302528.7_Frame_Shift_Ins_p.S1007fs|CLIP1_ENST00000358808.2_Frame_Shift_Ins_p.S1007fs|CLIP1_ENST00000537178.1_Frame_Shift_Ins_p.S972fs			P30622	CLIP1_HUMAN	CAP-GLY domain containing linker protein 1	1018					microtubule bundle formation (GO:0001578)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|positive regulation of microtubule polymerization (GO:0031116)|transport (GO:0006810)	cell projection (GO:0042995)|centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|intermediate filament (GO:0005882)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)	metal ion binding (GO:0046872)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|nucleic acid binding (GO:0003676)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|endometrium(4)|kidney(5)|large_intestine(16)|liver(1)|lung(21)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.81e-05)|Epithelial(86;6.85e-05)|BRCA - Breast invasive adenocarcinoma(302;0.226)		CTGGTTGTGGCTTGTTTCCATT	0.505																																						ENST00000358808.2																			0				NS(1)|breast(5)|endometrium(4)|kidney(5)|large_intestine(16)|liver(1)|lung(21)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	60						c.(3019-3021)ccafs		CAP-GLY domain containing linker protein 1																																				SO:0001589	frameshift_variant	6249				mitotic prometaphase|positive regulation of microtubule polymerization	centrosome|cytosol|endosome|intermediate filament|kinetochore	nucleic acid binding|protein homodimerization activity|zinc ion binding	g.chr12:122812690_122812691insT		CCDS9232.1, CCDS9233.1, CCDS58285.1	12q24.3	2013-01-17	2007-01-05	2007-01-05	ENSG00000130779	ENSG00000130779			10461	protein-coding gene	gene with protein product	"""restin"""	179838	"""restin (Reed-Steinberg cell-expressed intermediate filament-associated protein)"""	RSN		8222754	Standard	NM_001247997		Approved	CYLN1, CLIP170, CLIP, CLIP-170	uc001ucg.2	P30622	OTTHUMG00000168922	ENST00000540338.1:c.3053dupA	12.37:g.122812692_122812692dupT	ENSP00000439093:p.Ser1018fs					CLIP1_ENST00000302528.7_Frame_Shift_Ins_p.P1007fs|CLIP1_ENST00000540338.1_Frame_Shift_Ins_p.P1018fs|CLIP1_ENST00000545889.1_Frame_Shift_Ins_p.P593fs|CLIP1_ENST00000361654.4_Frame_Shift_Ins_p.P896fs|CLIP1_ENST00000537178.1_Frame_Shift_Ins_p.P972fs	p.P1007fs	NM_001247997.1|NM_002956.2	NP_001234926.1|NP_002947.1	P30622	CLIP1_HUMAN		OV - Ovarian serous cystadenocarcinoma(86;1.81e-05)|Epithelial(86;6.85e-05)|BRCA - Breast invasive adenocarcinoma(302;0.226)	16	3173_3174	-	all_neural(191;0.0837)|Medulloblastoma(191;0.163)		1018					A0AVD3|Q17RS4|Q29RG0	Frame_Shift_Ins	INS	ENST00000540338.1	37	c.3019_3020insA	CCDS58285.1																																																																																				0.505	CLIP1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000401625.1	NM_002956		11	1167						11	1167	---	---	---	---
ESRRAP2	144832	broad.mit.edu	37	13	21835723	21835728	+	RNA	DEL	GGCGAG	GGCGAG	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr13:21835723_21835728delGGCGAG	ENST00000427890.1	+	0	61									estrogen-related receptor alpha pseudogene 2																		GATGGACTGAGGCGAGGGGTGGGACT	0.646																																						ENST00000427890.1																			0																																																			0							g.chr13:21835723_21835728delGGCGAG	U85258		13q12.11	2011-03-15			ENSG00000235438	ENSG00000235438			24647	pseudogene	pseudogene						9344655, 3267207, 18065488	Standard	NG_007350		Approved	ESTRRA			OTTHUMG00000016534		13.37:g.21835723_21835728delGGCGAG														0	61	+									RNA	DEL	ENST00000427890.1	37																																																																																						0.646	ESRRAP2-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000471193.1	NR_000033		12	17						12	17	---	---	---	---
TPTE2P6	374491	broad.mit.edu	37	13	25157747	25157748	+	RNA	INS	-	-	T	rs74332804		TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr13:25157747_25157748insT	ENST00000453498.1	+	0	554				TPTE2P6_ENST00000440905.1_RNA																							AAAATGGGAGGTTTTTTTAGGG	0.411																																						ENST00000453498.1																			0																																																			0							g.chr13:25157747_25157748insT																													13.37:g.25157754_25157754dupT														0	554	+									RNA	INS	ENST00000453498.1	37																																																																																						0.411	RP11-556N21.1-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000044193.1			8	66						8	66	---	---	---	---
TSC22D1	8848	broad.mit.edu	37	13	45148691	45148693	+	In_Frame_Del	DEL	TGT	TGT	-	rs148625973|rs541782956	byFrequency	TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr13:45148691_45148693delTGT	ENST00000458659.2	-	1	2008_2010	c.1518_1520delACA	c.(1516-1521)caacag>cag	p.506_507QQ>Q	TSC22D1_ENST00000501704.2_In_Frame_Del_p.506_507QQ>Q|TSC22D1_ENST00000460842.1_5'Flank	NM_183422.3	NP_904358.2	Q15714	T22D1_HUMAN	TSC22 domain family, member 1	506	Gln-rich.				negative regulation of apoptotic process (GO:0043066)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_hematologic(4;8.74e-08)|Acute lymphoblastic leukemia(4;1.78e-07)|Lung NSC(96;2.21e-05)|Breast(139;0.000625)|Prostate(109;0.000947)|Hepatocellular(98;0.0202)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;0.000522)|BRCA - Breast invasive adenocarcinoma(63;0.118)		TGgttgttgctgttgttgttgtt	0.502														87	0.0173722	0.0598	0.0086	5008	,	,		24285	0.0		0.0	False		,,,				2504	0.002					ENST00000458659.2																			0				breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						c.(1516-1521)cag>ca		TSC22 domain family, member 1																																				SO:0001651	inframe_deletion	8848				transcription from RNA polymerase II promoter	cytoplasm|nucleus	protein binding|sequence-specific DNA binding transcription factor activity	g.chr13:45148691_45148693delTGT	AJ222700	CCDS9392.1, CCDS31966.1, CCDS58291.1, CCDS73565.1	13q14	2008-02-05	2005-03-01	2005-03-03	ENSG00000102804	ENSG00000102804			16826	protein-coding gene	gene with protein product		607715	"""transforming growth factor beta 1 induced transcript 4"""	TGFB1I4		8651929, 9022669	Standard	NM_183422		Approved	TSC22, MGC17597	uc001uzn.4	Q15714	OTTHUMG00000016838	ENST00000458659.2:c.1518_1520delACA	13.37:g.45148700_45148702delTGT	ENSP00000397435:p.Gln509del					TSC22D1_ENST00000501704.2_In_Frame_Del_p.QQ508del	p.QQ508del	NM_183422.3	NP_904358.2	Q15714	T22D1_HUMAN		GBM - Glioblastoma multiforme(144;0.000522)|BRCA - Breast invasive adenocarcinoma(63;0.118)	1	2008_2010	-		all_hematologic(4;8.74e-08)|Acute lymphoblastic leukemia(4;1.78e-07)|Lung NSC(96;2.21e-05)|Breast(139;0.000625)|Prostate(109;0.000947)|Hepatocellular(98;0.0202)|Lung SC(185;0.0262)	508			Gln-rich.		B3KRL7|B9EGI0|O00666|Q6AHX5|Q6IBU1|Q8NCN1|Q96JS5	In_Frame_Del	DEL	ENST00000458659.2	37	c.1518_1520delACA	CCDS31966.1																																																																																				0.502	TSC22D1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044743.2	NM_006022		10	743						10	743	---	---	---	---
TPTE2P2	644623	broad.mit.edu	37	13	52796688	52796688	+	RNA	DEL	C	C	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr13:52796688delC	ENST00000451298.1	-	0	1229				TPTE2P2_ENST00000606973.1_RNA																							cgctattgctccccacccatc	0.537																																						ENST00000451298.1																			0																																																			0							g.chr13:52796688delC																													13.37:g.52796688delC						RP11-64P12.8_ENST00000606031.1_RNA								0	1229	-									RNA	DEL	ENST00000451298.1	37																																																																																						0.537	RP11-248G5.8-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000471093.1			15	121						15	121	---	---	---	---
KIAA0391	9692	broad.mit.edu	37	14	35592700	35592700	+	Frame_Shift_Del	DEL	T	T	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr14:35592700delT	ENST00000557565.1	+	2	630	c.249delT	c.(247-249)catfs	p.H83fs	PPP2R3C_ENST00000555644.1_5'Flank|PPP2R3C_ENST00000261475.5_5'Flank|KIAA0391_ENST00000603544.1_Frame_Shift_Del_p.H83fs|KIAA0391_ENST00000605870.1_Intron|KIAA0391_ENST00000604948.1_Intron|KIAA0391_ENST00000534898.4_Frame_Shift_Del_p.H83fs|KIAA0391_ENST00000321130.10_Frame_Shift_Del_p.H83fs|KIAA0391_ENST00000250377.7_5'UTR|KIAA0391_ENST00000603588.1_Intron	NM_001282234.1	NP_001269163.1	O15091	MRRP3_HUMAN	KIAA0391	83					tRNA processing (GO:0008033)	mitochondrion (GO:0005739)				central_nervous_system(1)|endometrium(4)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	14	Breast(36;0.0545)|Hepatocellular(127;0.158)|Prostate(35;0.184)		Lung(238;2.93e-05)|LUAD - Lung adenocarcinoma(48;3.86e-05)|Epithelial(34;0.0114)|all cancers(34;0.0277)	GBM - Glioblastoma multiforme(112;0.0593)		CTGTTCCTCATTTTTTTTTAG	0.423																																						ENST00000557565.1																			0				central_nervous_system(1)|endometrium(4)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	14						c.(247-249)cafs		KIAA0391							49.0	48.0	48.0					14																	35592700		2203	4300	6503	SO:0001589	frameshift_variant	9692				tRNA processing	mitochondrion		g.chr14:35592700delT	AB002389	CCDS32063.1, CCDS58312.1, CCDS58313.1, CCDS58314.1	14q13.2	2013-06-18			ENSG00000100890	ENSG00000100890			19958	protein-coding gene	gene with protein product	"""mitochondrial RNase P subunit 3"", ""proteinaceous RNase P"""	609947				9205841, 18984158	Standard	NM_001256678		Approved	MRPP3, PRORP	uc001wsy.2	O15091		ENST00000557565.1:c.249delT	14.37:g.35592700delT	ENSP00000454657:p.His83fs					KIAA0391_ENST00000534898.4_Frame_Shift_Del_p.H83fs|KIAA0391_ENST00000603588.1_Intron|KIAA0391_ENST00000604948.1_Intron|KIAA0391_ENST00000603544.1_Frame_Shift_Del_p.H83fs|KIAA0391_ENST00000321130.10_Frame_Shift_Del_p.H83fs|KIAA0391_ENST00000250377.7_5'UTR|KIAA0391_ENST00000605870.1_Intron	p.H83fs			O15091	MRRP3_HUMAN	Lung(238;2.93e-05)|LUAD - Lung adenocarcinoma(48;3.86e-05)|Epithelial(34;0.0114)|all cancers(34;0.0277)	GBM - Glioblastoma multiforme(112;0.0593)	2	630	+	Breast(36;0.0545)|Hepatocellular(127;0.158)|Prostate(35;0.184)		83					B4DXD9|B4E0S8|B4E211|C4AM93|D3DS99|D3DSA1|Q86SZ4|Q86YB5|Q8N5L5	Frame_Shift_Del	DEL	ENST00000557565.1	37	c.249delT	CCDS32063.1																																																																																				0.423	KIAA0391-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000411280.1	NM_014672		12	296						12	296	---	---	---	---
FANCM	57697	broad.mit.edu	37	14	45642288	45642289	+	Frame_Shift_Del	DEL	CT	CT	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr14:45642288_45642289delCT	ENST00000267430.5	+	13	2276_2277	c.2191_2192delCT	c.(2191-2193)ctcfs	p.L731fs	FANCM_ENST00000542564.2_Frame_Shift_Del_p.L705fs	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	731					DNA repair (GO:0006281)|replication fork processing (GO:0031297)|resolution of meiotic recombination intermediates (GO:0000712)	FANCM-MHF complex (GO:0071821)|Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nuclease activity (GO:0004518)			breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(31)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	85						AATTCATCAACTCTCTCTCTCT	0.347								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																													ENST00000267430.5																			0				breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(31)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	85						c.(2191-2193)cfs	Involved in tolerance or repair of DNA crosslinks	Fanconi anemia, complementation group M																																				SO:0001589	frameshift_variant	57697	Fanconi Anemia	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	DNA repair	Fanconi anaemia nuclear complex	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding|nuclease activity|protein binding	g.chr14:45642288_45642289delCT	AK001672	CCDS32070.1	14q21.3	2014-09-17	2005-09-01	2005-09-01		ENSG00000187790		"""Fanconi anemia, complementation groups"""	23168	protein-coding gene	gene with protein product		609644	"""KIAA1596"""	KIAA1596		10997877, 16116422	Standard	NM_020937		Approved	FAAP250	uc001wwd.4	Q8IYD8		ENST00000267430.5:c.2191_2192delCT	14.37:g.45642298_45642299delCT	ENSP00000267430:p.Leu731fs					FANCM_ENST00000542564.2_Frame_Shift_Del_p.L705fs	p.L731fs	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN			13	2276_2277	+			731					B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Frame_Shift_Del	DEL	ENST00000267430.5	37	c.2191_2192delCT	CCDS32070.1																																																																																				0.347	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128		7	474						7	474	---	---	---	---
HSPA2	3306	broad.mit.edu	37	14	65002366	65002367	+	5'Flank	INS	-	-	T	rs45532333		TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr14:65002366_65002367insT	ENST00000394709.1	+	0	0				RP11-973N13.4_ENST00000554918.1_RNA			P54652	HSP72_HUMAN	heat shock 70kDa protein 2						male meiosis (GO:0007140)|male meiosis I (GO:0007141)|negative regulation of inclusion body assembly (GO:0090084)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G2/M transition of mitotic cell cycle (GO:0031662)|protein refolding (GO:0042026)|response to unfolded protein (GO:0006986)|spermatid development (GO:0007286)|synaptonemal complex disassembly (GO:0070194)	blood microparticle (GO:0072562)|CatSper complex (GO:0036128)|cell surface (GO:0009986)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|male germ cell nucleus (GO:0001673)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|glycolipid binding (GO:0051861)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(4)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	22				all cancers(60;0.00515)|OV - Ovarian serous cystadenocarcinoma(108;0.00584)|BRCA - Breast invasive adenocarcinoma(234;0.045)		GTAAGATCTGATTTTTTTTTCA	0.436																																					Pancreas(136;1211 1835 24894 31984 38227)	ENST00000554918.1																			0																																																	SO:0001631	upstream_gene_variant	0							g.chr14:65002366_65002367insT	L26336, BC001752	CCDS9766.1	14q23	2012-10-02	2002-08-29		ENSG00000126803	ENSG00000126803		"""Heat shock proteins / HSP70"""	5235	protein-coding gene	gene with protein product		140560	"""heat shock 70kD protein 2"""				Standard	NM_021979		Approved		uc001xhk.4	P54652	OTTHUMG00000141311		14.37:g.65002375_65002375dupT	Exception_encountered													0	52	-								Q15508|Q53XM3|Q9UE78	RNA	INS	ENST00000394709.1	37		CCDS9766.1																																																																																				0.436	HSPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280651.1			7	186						7	186	---	---	---	---
RBM25	58517	broad.mit.edu	37	14	73572607	73572608	+	Frame_Shift_Del	DEL	AG	AG	-	rs150988201		TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr14:73572607_73572608delAG	ENST00000261973.7	+	11	1480_1481	c.1195_1196delAG	c.(1195-1197)agafs	p.R399fs	RBM25_ENST00000527432.1_Frame_Shift_Del_p.R399fs	NM_021239.2	NP_067062.1	P49756	RBM25_HUMAN	RNA binding motif protein 25	399	Arg-rich.|Glu-rich.|Necessary for nuclear speckle localization.				mRNA processing (GO:0006397)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of apoptotic process (GO:0042981)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(6)|ovary(2)|pancreas(1)	31				BRCA - Breast invasive adenocarcinoma(234;0.00362)|OV - Ovarian serous cystadenocarcinoma(108;0.0688)		agagcgggaaagagagagagag	0.446																																						ENST00000261973.7																			0				breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(6)|ovary(2)|pancreas(1)	31						c.(1195-1197)afs		RNA binding motif protein 25																																				SO:0001589	frameshift_variant	58517				apoptosis|mRNA processing|regulation of alternative nuclear mRNA splicing, via spliceosome|RNA splicing	cytoplasm|nuclear speck	mRNA binding|nucleotide binding|protein binding	g.chr14:73572607_73572608delAG	BX647116	CCDS32113.1	14q24.3	2013-02-12	2004-04-23	2004-04-29	ENSG00000119707	ENSG00000119707		"""RNA binding motif (RRM) containing"""	23244	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 94"""	612427	"""RNA-binding region (RNP1, RRM) containing 7"""	RNPC7		9847074, 7596406	Standard	NM_021239		Approved	S164, fSAP94, NET52, Snu71	uc001xno.3	P49756	OTTHUMG00000167540	ENST00000261973.7:c.1195_1196delAG	14.37:g.73572617_73572618delAG	ENSP00000261973:p.Arg399fs					RBM25_ENST00000527432.1_Frame_Shift_Del_p.R399fs	p.R399fs	NM_021239.2	NP_067062.1	P49756	RBM25_HUMAN		BRCA - Breast invasive adenocarcinoma(234;0.00362)|OV - Ovarian serous cystadenocarcinoma(108;0.0688)	11	1480_1481	+			399			Arg-rich.|Glu-rich.|Necessary for nuclear speckle localization.		A0PJL9|B2RNA8|B3KT03|Q2TA72|Q5XJ17|Q6P665|Q9H6A1|Q9UEQ5|Q9UIE9	Frame_Shift_Del	DEL	ENST00000261973.7	37	c.1195_1196delAG	CCDS32113.1																																																																																				0.446	RBM25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394966.1	XM_027330		10	204						10	204	---	---	---	---
ELMSAN1	91748	broad.mit.edu	37	14	74205926	74205928	+	In_Frame_Del	DEL	CTG	CTG	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr14:74205926_74205928delCTG	ENST00000286523.5	-	2	1566_1568	c.784_786delCAG	c.(784-786)cagdel	p.Q262del	ELMSAN1_ENST00000394071.2_In_Frame_Del_p.Q262del|ELMSAN1_ENST00000486739.1_5'Flank	NM_194278.3	NP_919254.2	Q6PJG2	EMSA1_HUMAN	ELM2 and Myb/SANT-like domain containing 1	262	Gln-rich.|Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)										GTAGGgctgcctgctgctgctgc	0.65																																						ENST00000286523.5																			0											c.(784-786)del		ELM2 and Myb/SANT-like domain containing 1																																				SO:0001651	inframe_deletion	91748							g.chr14:74205926_74205928delCTG	BF971739	CCDS9819.1	14q24.3	2012-09-25	2012-09-25	2012-09-25	ENSG00000156030	ENSG00000156030			19853	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 117"", ""chromosome 14 open reading frame 43"""	C14orf117, C14orf43			Standard	NM_194278		Approved	LSR68	uc001xou.3	Q6PJG2	OTTHUMG00000150359	ENST00000286523.5:c.784_786delCAG	14.37:g.74205935_74205937delCTG	ENSP00000286523:p.Gln262del					ELMSAN1_ENST00000394071.2_In_Frame_Del_p.Q262del	p.Q262del	NM_194278.3	NP_919254.2					2	1566_1568	-								Q6PK13|Q6PK59|Q6ZS23	In_Frame_Del	DEL	ENST00000286523.5	37	c.784_786delCAG	CCDS9819.1																																																																																				0.650	ELMSAN1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317793.1	NM_194278		10	220						10	220	---	---	---	---
MLH3	27030	broad.mit.edu	37	14	75514604	75514604	+	Frame_Shift_Del	DEL	T	T	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr14:75514604delT	ENST00000556740.1	-	1	1790	c.1755delA	c.(1753-1755)aaafs	p.K585fs	MLH3_ENST00000380968.2_5'UTR|MLH3_ENST00000544985.1_5'Flank|MLH3_ENST00000556257.1_Frame_Shift_Del_p.K585fs|MLH3_ENST00000555671.1_5'Flank|MLH3_ENST00000355774.2_Frame_Shift_Del_p.K585fs|MLH3_ENST00000238662.7_Frame_Shift_Del_p.K585fs			Q9UHC1	MLH3_HUMAN	mutL homolog 3	585					ATP catabolic process (GO:0006200)|female meiosis I (GO:0007144)|male meiosis (GO:0007140)|mismatch repair (GO:0006298)|protein localization (GO:0008104)|reciprocal meiotic recombination (GO:0007131)|synaptonemal complex assembly (GO:0007130)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|mismatch repair complex (GO:0032300)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|centromeric DNA binding (GO:0019237)|chromatin binding (GO:0003682)|mismatched DNA binding (GO:0030983)|satellite DNA binding (GO:0003696)|single-stranded DNA binding (GO:0003697)	p.A577_S588delAQTEKEKKKESS(2)		breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	44				BRCA - Breast invasive adenocarcinoma(234;0.00688)		TGCTAGATTCTTTTTTTTTCT	0.358								Mismatch excision repair (MMR)																														ENST00000355774.2																			2	Deletion - In frame(2)	p.A577_S588delAQTEKEKKKESS(2)	breast(2)	breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	44						c.(1753-1755)aafs	Mismatch excision repair (MMR)	mutL homolog 3							115.0	116.0	116.0					14																	75514604		2203	4300	6503	SO:0001589	frameshift_variant	27030				mismatch repair|reciprocal meiotic recombination	chiasma|MutLbeta complex|synaptonemal complex	ATP binding|ATPase activity|mismatched DNA binding|protein binding|satellite DNA binding	g.chr14:75514604delT	AF195657	CCDS9837.1, CCDS32123.1	14q24.3	2014-09-17	2013-09-12			ENSG00000119684			7128	protein-coding gene	gene with protein product		604395	"""mutL (E. coli) homolog 3"", ""mutL homolog 3 (E. coli)"""			10615123	Standard	XR_245681		Approved		uc001xrd.1	Q9UHC1		ENST00000556740.1:c.1755delA	14.37:g.75514604delT	ENSP00000452316:p.Lys585fs					MLH3_ENST00000238662.7_Frame_Shift_Del_p.K585fs|MLH3_ENST00000556740.1_Frame_Shift_Del_p.K585fs|MLH3_ENST00000556257.1_Frame_Shift_Del_p.K585fs|MLH3_ENST00000380968.2_5'UTR	p.K585fs	NM_001040108.1	NP_001035197.1	Q9UHC1	MLH3_HUMAN		BRCA - Breast invasive adenocarcinoma(234;0.00688)	2	1970	-			585					P49751|Q56DK9|Q9P292|Q9UHC0	Frame_Shift_Del	DEL	ENST00000556740.1	37	c.1755delA	CCDS32123.1																																																																																				0.358	MLH3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415006.1	NM_014381		12	644						12	644	---	---	---	---
SYNE3	161176	broad.mit.edu	37	14	95921888	95921890	+	In_Frame_Del	DEL	CTC	CTC	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr14:95921888_95921890delCTC	ENST00000334258.5	-	5	975_977	c.961_963delGAG	c.(961-963)gagdel	p.E321del	SYNE3_ENST00000554873.1_In_Frame_Del_p.E78del|SYNE3_ENST00000553340.1_In_Frame_Del_p.E321del|SYNE3_ENST00000557275.1_In_Frame_Del_p.E321del	NM_152592.3	NP_689805.3	Q6ZMZ3	SYNE3_HUMAN	spectrin repeat containing, nuclear envelope family member 3	321					cytoskeletal anchoring at nuclear membrane (GO:0090286)|cytoskeleton organization (GO:0007010)|establishment of protein localization to membrane (GO:0090150)|regulation of cell shape (GO:0008360)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear outer membrane (GO:0005640)|SUN-KASH complex (GO:0034993)	actin filament binding (GO:0051015)			breast(1)|endometrium(2)|lung(25)	28						CCCGCAGCCGCTCCTCCTCCTCC	0.616																																						ENST00000334258.5																			0				breast(1)|endometrium(2)|lung(25)	28						c.(961-963)del		spectrin repeat containing, nuclear envelope family member 3																																				SO:0001651	inframe_deletion	161176							g.chr14:95921888_95921890delCTC	AK098471	CCDS9935.1	14q32.13	2012-05-31	2012-05-31	2012-05-31	ENSG00000176438	ENSG00000176438			19861	protein-coding gene	gene with protein product		610861	"""chromosome 14 open reading frame 49"""	C14orf49			Standard	NM_152592		Approved	FLJ25605, NET53, Nesprin-3, Nesp3	uc001yei.4	Q6ZMZ3	OTTHUMG00000171632	ENST00000334258.5:c.961_963delGAG	14.37:g.95921897_95921899delCTC	ENSP00000334308:p.Glu321del					SYNE3_ENST00000554873.1_In_Frame_Del_p.E78del|SYNE3_ENST00000553340.1_In_Frame_Del_p.E321del|SYNE3_ENST00000557275.1_In_Frame_Del_p.E321del	p.E321del	NM_152592.3	NP_689805.3					5	975_977	-								A6H8H3|Q86SX5|Q8N7G8	In_Frame_Del	DEL	ENST00000334258.5	37	c.961_963delGAG	CCDS9935.1																																																																																				0.616	SYNE3-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420529.2	NM_152592		7	806						7	806	---	---	---	---
YY1	7528	broad.mit.edu	37	14	100705708	100705710	+	In_Frame_Del	DEL	GAG	GAG	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr14:100705708_100705710delGAG	ENST00000262238.4	+	1	387_389	c.127_129delGAG	c.(127-129)gagdel	p.E47del	RP11-638I2.4_ENST00000554537.1_RNA	NM_003403.3	NP_003394.1	P25490	TYY1_HUMAN	YY1 transcription factor	47	Asp/Glu-rich (acidic).|Interaction with the SMAD1/SMAD4 complex.				anterior/posterior pattern specification (GO:0009952)|camera-type eye morphogenesis (GO:0048593)|cell differentiation (GO:0030154)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|chromosome organization (GO:0051276)|double-strand break repair via homologous recombination (GO:0000724)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to prostaglandin F (GO:0034696)|response to UV-C (GO:0010225)|RNA localization (GO:0006403)|spermatogenesis (GO:0007283)	Ino80 complex (GO:0031011)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|four-way junction DNA binding (GO:0000400)|RNA binding (GO:0003723)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.E43delE(1)		cervix(1)|endometrium(1)|large_intestine(1)|liver(2)|lung(1)|prostate(4)|skin(1)	11		Melanoma(154;0.152)				AGTggtgggcgaggaggaggagg	0.719																																						ENST00000262238.4																			1	Deletion - In frame(1)	p.E43delE(1)	prostate(1)	cervix(1)|endometrium(1)|large_intestine(1)|liver(2)|lung(1)|prostate(4)|skin(1)	11						c.(127-129)del		YY1 transcription factor				381,3745		7,367,1689						1.4	0.5			18	569,7489		8,553,3468	no	coding	YY1	NM_003403.3		15,920,5157	A1A1,A1R,RR		7.0613,9.2341,7.7971				950,11234				SO:0001651	inframe_deletion	7528				cell differentiation|cellular response to UV|double-strand break repair via homologous recombination|negative regulation of transcription from RNA polymerase II promoter|response to UV-C|spermatogenesis	Ino80 complex|nuclear matrix|plasma membrane	four-way junction DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity|transcription regulatory region DNA binding|zinc ion binding	g.chr14:100705708_100705710delGAG	BC020324	CCDS9957.1	14q	2013-01-08			ENSG00000100811	ENSG00000100811		"""INO80 complex subunits"", ""Zinc fingers, C2H2-type"""	12856	protein-coding gene	gene with protein product	"""INO80 complex subunit S"", ""Yin and Yang 1 protein"""	600013				1655281, 7912122	Standard	NM_003403		Approved	NF-E1, DELTA, UCRBP, YIN-YANG-1, INO80S	uc001ygy.2	P25490	OTTHUMG00000150479	ENST00000262238.4:c.127_129delGAG	14.37:g.100705717_100705719delGAG	ENSP00000262238:p.Glu47del						p.E47del	NM_003403.3	NP_003394.1	P25490	TYY1_HUMAN			1	387_389	+		Melanoma(154;0.152)	47			Asp/Glu-rich (acidic).		Q14935	In_Frame_Del	DEL	ENST00000262238.4	37	c.127_129delGAG	CCDS9957.1																																																																																				0.719	YY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318277.1	NM_003403		7	82						7	82	---	---	---	---
IGHJ6	28475	broad.mit.edu	37	14	106329451	106329453	+	RNA	DEL	GTA	GTA	-	rs373021870|rs2338626|rs2338627|rs67183528|rs2338628|rs376479093	byFrequency	TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr14:106329451_106329453delGTA	ENST00000390560.2	-	0	15_17				IGHJ1_ENST00000390565.1_RNA|IGHJ2_ENST00000390564.2_RNA|IGHJ3_ENST00000463911.1_RNA|IGHJ4_ENST00000461719.1_RNA|IGHD7-27_ENST00000439842.1_RNA|IGHJ5_ENST00000488476.1_RNA					immunoglobulin heavy joining 6																		AGACGTCCATGTAGTAGTAGTAG	0.537																																						ENST00000390560.2																			0																																																			0							g.chr14:106329451_106329453delGTA	J00256		14q32.33	2012-02-08			ENSG00000211900	ENSG00000211900		"""Immunoglobulins / IGH locus"""	5540	other	immunoglobulin gene							Standard	NG_001019		Approved				OTTHUMG00000152455		14.37:g.106329460_106329462delGTA														0	15_17	-									RNA	DEL	ENST00000390560.2	37																																																																																						0.537	IGHJ6-001	KNOWN	mRNA_start_NF|mRNA_end_NF|cds_start_NF|cds_end_NF|basic|appris_principal	IG_J_gene	IG_J_gene	OTTHUMT00000326277.1	NG_001019		8	696						8	696	---	---	---	---
IGHV4-39	28394	broad.mit.edu	37	14	106877821	106877826	+	RNA	DEL	CTACTG	CTACTG	-	rs371574132|rs587704823|rs377249313|rs587658822|rs587600484|rs374128985|rs587603411	byFrequency	TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr14:106877821_106877826delCTACTG	ENST00000390619.2	-	0	217_222									immunoglobulin heavy variable 4-39																		GTAGTAACTACTACTGCTGATGGAGC	0.607																																						ENST00000390619.2																			0																	59,3537		4,51,1743						-0.2	0.0		dbSNP_134	57	122,7696		12,98,3799	no	intergenic				16,149,5542	A1A1,A1R,RR		1.5605,1.6407,1.5858				181,11233						0							g.chr14:106877821_106877826delCTACTG	L10094		14q32.33	2012-02-08			ENSG00000211959	ENSG00000211959		"""Immunoglobulins / IGH locus"""	5651	other	immunoglobulin gene							Standard	NG_001019		Approved				OTTHUMG00000152067		14.37:g.106877821_106877826delCTACTG														0	217_222	-									RNA	DEL	ENST00000390619.2	37																																																																																						0.607	IGHV4-39-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene	OTTHUMT00000325161.1	NG_001019		7	537						7	537	---	---	---	---
HERC2	8924	broad.mit.edu	37	15	28518115	28518115	+	Frame_Shift_Del	DEL	C	C	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr15:28518115delC	ENST00000261609.7	-	8	944	c.836delG	c.(835-837)ggafs	p.G279fs		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2									p.G279V(1)|p.G279fs*25(1)		NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		GGGGATGCTTCCTGGCCCTTT	0.592																																						ENST00000261609.7																			2	Substitution - Missense(1)|Deletion - Frameshift(1)	p.G279V(1)|p.G279fs*25(1)	autonomic_ganglia(1)|breast(1)	NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204						c.(835-837)gafs		HECT and RLD domain containing E3 ubiquitin protein ligase 2							50.0	48.0	49.0					15																	28518115		2203	4300	6503	SO:0001589	frameshift_variant	8924				DNA repair|intracellular protein transport|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus	guanyl-nucleotide exchange factor activity|heme binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding	g.chr15:28518115delC	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"""hect domain and RLD 2"""			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.836delG	15.37:g.28518115delC	ENSP00000261609:p.Gly279fs						p.G279fs	NM_004667.5	NP_004658.3	O95714	HERC2_HUMAN		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)	8	944	-		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)	279						Frame_Shift_Del	DEL	ENST00000261609.7	37	c.836delG	CCDS10021.1																																																																																				0.592	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		10	308						10	308	---	---	---	---
SPATA5L1	79029	broad.mit.edu	37	15	45710840	45710841	+	Frame_Shift_Ins	INS	-	-	T			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr15:45710840_45710841insT	ENST00000305560.6	+	7	2153_2154	c.2054_2055insT	c.(2053-2058)tgttttfs	p.CF685fs	SPATA5L1_ENST00000533841.1_3'UTR	NM_024063.2	NP_076968.2	Q9BVQ7	SPA5L_HUMAN	spermatogenesis associated 5-like 1	685						cytoplasm (GO:0005737)	ATP binding (GO:0005524)			kidney(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	14		Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;7.31e-17)|GBM - Glioblastoma multiforme(94;6.28e-07)		GCAGAAACCTGTTTTTTTTCTG	0.361																																						ENST00000305560.6																			0				kidney(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	14						c.(2053-2055)tttfs		spermatogenesis associated 5-like 1																																				SO:0001589	frameshift_variant	79029					cytoplasm	ATP binding|nucleoside-triphosphatase activity	g.chr15:45710840_45710841insT	AK023232	CCDS10123.1	15q15.1	2010-04-21			ENSG00000171763	ENSG00000171763		"""ATPases / AAA-type"""	28762	protein-coding gene	gene with protein product						12477932	Standard	NM_024063		Approved	MGC5347, FLJ12286	uc001zve.3	Q9BVQ7	OTTHUMG00000131425	ENST00000305560.6:c.2062dupT	15.37:g.45710848_45710848dupT	ENSP00000305494:p.Cys685fs					SPATA5L1_ENST00000533841.1_3'UTR	p.F685fs	NM_024063.2	NP_076968.2	Q9BVQ7	SPA5L_HUMAN		all cancers(107;7.31e-17)|GBM - Glioblastoma multiforme(94;6.28e-07)	7	2153_2154	+		Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)	685					C9JHR5|Q9H8W7|Q9HA41	Frame_Shift_Ins	INS	ENST00000305560.6	37	c.2054_2055insT	CCDS10123.1																																																																																				0.361	SPATA5L1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000254218.1	NM_024063		9	478						9	478	---	---	---	---
BLM	641	broad.mit.edu	37	15	91304138	91304139	+	Frame_Shift_Ins	INS	-	-	A	rs367543043		TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr15:91304138_91304139insA	ENST00000355112.3	+	7	1653_1654	c.1535_1536insA	c.(1534-1539)ggaaaafs	p.GK512fs	BLM_ENST00000560509.1_Frame_Shift_Ins_p.GK512fs	NM_000057.2	NP_000048.1	P54132	BLM_HUMAN	Bloom syndrome, RecQ helicase-like	512	Necessary for interaction with SPIDR.				alpha-beta T cell differentiation (GO:0046632)|ATP catabolic process (GO:0006200)|cellular response to camptothecin (GO:0072757)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hydroxyurea (GO:0072711)|cellular response to ionizing radiation (GO:0071479)|DNA double-strand break processing (GO:0000729)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA strand renaturation (GO:0000733)|double-strand break repair via homologous recombination (GO:0000724)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of cell division (GO:0051782)|negative regulation of DNA recombination (GO:0045910)|negative regulation of mitotic recombination (GO:0045950)|negative regulation of thymocyte apoptotic process (GO:0070244)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of transcription, DNA-templated (GO:0045893)|protein oligomerization (GO:0051259)|regulation of binding (GO:0051098)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|replication fork processing (GO:0031297)|replication fork protection (GO:0048478)|response to X-ray (GO:0010165)|telomere maintenance (GO:0000723)	cytoplasm (GO:0005737)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|nuclear chromosome (GO:0000228)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PML body (GO:0016605)|pronucleus (GO:0045120)|replication fork (GO:0005657)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent helicase activity (GO:0008026)|ATPase activity (GO:0016887)|bubble DNA binding (GO:0000405)|four-way junction helicase activity (GO:0009378)|G-quadruplex DNA binding (GO:0051880)|helicase activity (GO:0004386)|p53 binding (GO:0002039)|single-stranded DNA binding (GO:0003697)	p.N515fs*16(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(11)|liver(4)|lung(9)|ovary(6)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	Lung NSC(78;0.0875)|all_lung(78;0.109)		Lung(145;0.189)			CCAAGACTAGGAAAAAAAAATG	0.371			"""Mis, N, F"""			"""leukemia, lymphoma, skin squamous cell , other cancers"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Bloom syndrome																													ENST00000355112.3			yes	Rec		Bloom Syndrome	15	15q26.1	641	"""Mis, N, F"""	Bloom Syndrome			"""L, E"""		"""leukemia, lymphoma, skin squamous cell , other cancers"""			1	Deletion - Frameshift(1)	p.N515fs*16(1)	ovary(1)	breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(11)|liver(4)|lung(9)|ovary(6)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51						c.(1534-1536)gaafs	Genes defective in diseases associated with sensitivity to DNA damaging agents	Bloom syndrome, RecQ helicase-like																																				SO:0001589	frameshift_variant	641	Bloom syndrome	Familial Cancer Database		double-strand break repair via homologous recombination|G2 phase of mitotic cell cycle|G2/M transition DNA damage checkpoint|negative regulation of cell division|positive regulation of transcription, DNA-dependent|protein oligomerization|regulation of cyclin-dependent protein kinase activity|replication fork processing|replication fork protection|response to X-ray	cytoplasm|lateral element|nuclear matrix|nucleolus|PML body	ATP binding|bubble DNA binding|DNA strand annealing activity|four-way junction helicase activity|G-quadruplex DNA binding|p53 binding	g.chr15:91304138_91304139insA	U39817	CCDS10363.1, CCDS73782.1	15q26.1	2014-09-17	2009-03-19		ENSG00000197299	ENSG00000197299			1058	protein-coding gene	gene with protein product		604610	"""Bloom syndrome"""			9388193	Standard	NM_000057		Approved	BS, RECQL3, RECQ2	uc002bpr.3	P54132	OTTHUMG00000149834	ENST00000355112.3:c.1544dupA	15.37:g.91304147_91304147dupA	ENSP00000347232:p.Gly512fs					BLM_ENST00000560509.1_Frame_Shift_Ins_p.E512fs	p.E512fs	NM_000057.2	NP_000048.1	P54132	BLM_HUMAN	Lung(145;0.189)		7	1653_1654	+	Lung NSC(78;0.0875)|all_lung(78;0.109)		512					Q52M96	Frame_Shift_Ins	INS	ENST00000355112.3	37	c.1535_1536insA	CCDS10363.1																																																																																				0.371	BLM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313495.1			10	466						10	466	---	---	---	---
CHD2	1106	broad.mit.edu	37	15	93540316	93540316	+	Frame_Shift_Del	DEL	A	A	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr15:93540316delA	ENST00000394196.4	+	29	4793	c.3725delA	c.(3724-3726)gaafs	p.E1242fs	CHD2_ENST00000557381.1_Frame_Shift_Del_p.E1242fs	NM_001271.3	NP_001262.3	O14647	CHD2_HUMAN	chromodomain helicase DNA binding protein 2	1242					cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|hematopoietic stem cell differentiation (GO:0060218)|muscle organ development (GO:0007517)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|histone binding (GO:0042393)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(10)|lung(17)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	47	Lung NSC(78;0.00976)|all_lung(78;0.016)		BRCA - Breast invasive adenocarcinoma(143;0.0282)|OV - Ovarian serous cystadenocarcinoma(32;0.0814)			GACCCTGAAGAAAAAAAAAAG	0.348																																						ENST00000394196.4																			0				breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(10)|lung(17)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	47						c.(3724-3726)gafs		chromodomain helicase DNA binding protein 2							75.0	74.0	75.0					15																	93540316		2197	4298	6495	SO:0001589	frameshift_variant	1106				regulation of transcription from RNA polymerase II promoter	nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding	g.chr15:93540316delA	AF006514	CCDS10374.2, CCDS45356.1	15q26	2008-07-18			ENSG00000173575	ENSG00000173575			1917	protein-coding gene	gene with protein product		602119				9326634	Standard	NM_001042572		Approved	FLJ38614, DKFZp547I1315, DKFZp781D1727, DKFZp686E01200	uc002bsp.3	O14647	OTTHUMG00000149845	ENST00000394196.4:c.3725delA	15.37:g.93540316delA	ENSP00000377747:p.Glu1242fs					CHD2_ENST00000557381.1_Frame_Shift_Del_p.E1242fs	p.E1242fs	NM_001271.3	NP_001262.3	O14647	CHD2_HUMAN	BRCA - Breast invasive adenocarcinoma(143;0.0282)|OV - Ovarian serous cystadenocarcinoma(32;0.0814)		29	4793	+	Lung NSC(78;0.00976)|all_lung(78;0.016)		1242					C6G482|Q96IP5	Frame_Shift_Del	DEL	ENST00000394196.4	37	c.3725delA	CCDS10374.2																																																																																				0.348	CHD2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313528.3	NM_001271		12	386						12	386	---	---	---	---
RP11-266O8.1	0	broad.mit.edu	37	15	93974509	93974510	+	lincRNA	DEL	TC	TC	-	rs376790777|rs57286078|rs534087513|rs552210225	byFrequency	TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr15:93974509_93974510delTC	ENST00000543286.1	+	0	545																											TTGGCTGGGTTCtttttttttt	0.431																																						ENST00000543286.1																			0																																																			0							g.chr15:93974509_93974510delTC																													15.37:g.93974509_93974510delTC														0	545	+									RNA	DEL	ENST00000543286.1	37																																																																																						0.431	RP11-266O8.1-003	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000415156.1			7	225						7	225	---	---	---	---
BRICD5	283870	broad.mit.edu	37	16	2260586	2260588	+	In_Frame_Del	DEL	CAG	CAG	-	rs371145262		TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr16:2260586_2260588delCAG	ENST00000562360.1	-	2	114_116	c.115_117delCTG	c.(115-117)ctgdel	p.L39del	BRICD5_ENST00000566018.1_In_Frame_Del_p.L39del|BRICD5_ENST00000328540.3_In_Frame_Del_p.L39del|RP11-304L19.8_ENST00000561544.1_lincRNA			Q6PL45	BRID5_HUMAN	BRICHOS domain containing 5	39						integral component of membrane (GO:0016021)											CGGCcagcaccagcagcagcagc	0.66																																						ENST00000328540.3																			0											c.(115-117)del		BRICHOS domain containing 5																																				SO:0001651	inframe_deletion	283870							g.chr16:2260586_2260588delCAG	BC039154	CCDS10463.1	16p13.3	2012-10-10	2012-10-10	2012-10-10	ENSG00000182685	ENSG00000182685		"""BRICHOS domain containing"""	28309	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 79"""	C16orf79		12477932	Standard	NM_182563		Approved	MGC21830	uc002cpi.2	Q6PL45	OTTHUMG00000128831	ENST00000562360.1:c.115_117delCTG	16.37:g.2260595_2260597delCAG	ENSP00000455052:p.Leu39del					BRICD5_ENST00000562360.1_In_Frame_Del_p.L39del|BRICD5_ENST00000566018.1_In_Frame_Del_p.L39del	p.L39del	NM_182563.3	NP_872369.2					2	1231_1233	-								C9J7K2|Q8IXU9	In_Frame_Del	DEL	ENST00000562360.1	37	c.115_117delCTG	CCDS10463.1																																																																																				0.660	BRICD5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000435091.1	NM_182563		7	195						7	195	---	---	---	---
SLC5A11	115584	broad.mit.edu	37	16	24921737	24921739	+	In_Frame_Del	DEL	CAG	CAG	-	rs140499762		TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr16:24921737_24921739delCAG	ENST00000347898.3	+	15	2383_2385	c.1761_1763delCAG	c.(1759-1764)gccagc>gcc	p.S592del	SLC5A11_ENST00000545376.1_In_Frame_Del_p.S522del|SLC5A11_ENST00000424767.2_In_Frame_Del_p.S557del|SLC5A11_ENST00000449109.2_In_Frame_Del_p.S436del|SLC5A11_ENST00000568579.1_In_Frame_Del_p.S522del|SLC5A11_ENST00000539472.1_In_Frame_Del_p.S528del|SLC5A11_ENST00000569071.1_In_Frame_Del_p.S436del|SLC5A11_ENST00000567758.1_In_Frame_Del_p.S557del|SLC5A11_ENST00000565769.1_In_Frame_Del_p.S528del	NM_052944.3	NP_443176.2			solute carrier family 5 (sodium/inositol cotransporter), member 11											endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(30)|ovary(2)|prostate(2)|urinary_tract(1)	49				GBM - Glioblastoma multiforme(48;0.0365)		TGCCAGAGGCCAGCAGCAGCAGC	0.542																																						ENST00000347898.3																			0				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(30)|ovary(2)|prostate(2)|urinary_tract(1)	49						c.(1759-1764)gcc>gc		solute carrier family 5 (sodium/inositol cotransporter), member 11				0,59,4205		0,0,0,0,59,2073						2.3	0.0		dbSNP_134	91	12,151,8089		0,0,12,0,151,3963	no	codingComplex	SLC5A11	NM_052944.2		0,0,12,0,210,6036	A1A1,A1A2,A1R,A2A2,A2R,RR		1.9753,1.3837,1.7737				12,210,12294				SO:0001651	inframe_deletion	115584				apoptosis|carbohydrate transport|sodium ion transport	integral to membrane|plasma membrane	polyol transmembrane transporter activity|symporter activity	g.chr16:24921737_24921739delCAG	AF292385	CCDS10625.1, CCDS58437.1, CCDS58438.1, CCDS58439.1, CCDS58440.1	16p12.1	2013-07-19	2013-07-19		ENSG00000158865	ENSG00000158865		"""Solute carriers"""	23091	protein-coding gene	gene with protein product		610238	"""solute carrier family 5 (sodium/glucose cotransporter), member 11"""			12039040, 12133831	Standard	NM_001258414		Approved	KST1, SMIT2, SGLT6	uc002dmu.4	Q8WWX8	OTTHUMG00000097003	ENST00000347898.3:c.1761_1763delCAG	16.37:g.24921746_24921748delCAG	ENSP00000289932:p.Ser592del					SLC5A11_ENST00000545376.1_In_Frame_Del_p.AS517del|SLC5A11_ENST00000569071.1_In_Frame_Del_p.AS431del|SLC5A11_ENST00000539472.1_In_Frame_Del_p.AS523del|SLC5A11_ENST00000568579.1_In_Frame_Del_p.AS517del|SLC5A11_ENST00000565769.1_In_Frame_Del_p.AS523del|SLC5A11_ENST00000449109.2_In_Frame_Del_p.AS431del|SLC5A11_ENST00000424767.2_In_Frame_Del_p.AS552del|SLC5A11_ENST00000567758.1_In_Frame_Del_p.AS552del	p.AS587del	NM_052944.3	NP_443176.2	Q8WWX8	SC5AB_HUMAN		GBM - Glioblastoma multiforme(48;0.0365)	15	2383_2385	+			587						In_Frame_Del	DEL	ENST00000347898.3	37	c.1761_1763delCAG	CCDS10625.1																																																																																				0.542	SLC5A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214091.3	NM_052944		16	413						16	413	---	---	---	---
IL4R	3566	broad.mit.edu	37	16	27373787	27373789	+	In_Frame_Del	DEL	GAG	GAG	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr16:27373787_27373789delGAG	ENST00000395762.2	+	11	1373_1375	c.1114_1116delGAG	c.(1114-1116)gagdel	p.E376del	IL4R_ENST00000170630.2_In_Frame_Del_p.E376del|IL4R_ENST00000565915.1_3'UTR|IL4R_ENST00000543915.2_In_Frame_Del_p.E376del|IL4R_ENST00000380922.3_In_Frame_Del_p.E361del	NM_000418.3	NP_000409.1	P24394	IL4RA_HUMAN	interleukin 4 receptor	376	Poly-Glu.				defense response to protozoan (GO:0042832)|immune response (GO:0006955)|interleukin-4-mediated signaling pathway (GO:0035771)|intracellular signal transduction (GO:0035556)|negative regulation of T-helper 1 cell differentiation (GO:0045626)|ovulation (GO:0030728)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of macrophage activation (GO:0043032)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|production of molecular mediator involved in inflammatory response (GO:0002532)|regulation of cell proliferation (GO:0042127)|response to estrogen (GO:0043627)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	interleukin-4 receptor activity (GO:0004913)|receptor signaling protein activity (GO:0005057)			breast(3)|endometrium(2)|kidney(2)|large_intestine(2)|lung(15)|ovary(2)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	33						GGTGGAGTGTGAGGAGGAGGAGG	0.591																																						ENST00000395762.2																			0				breast(3)|endometrium(2)|kidney(2)|large_intestine(2)|lung(15)|ovary(2)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	33						c.(1114-1116)del		interleukin 4 receptor																																				SO:0001651	inframe_deletion	3566				immune response|production of molecular mediator involved in inflammatory response	integral to plasma membrane	identical protein binding|interleukin-4 receptor activity|receptor signaling protein activity	g.chr16:27373787_27373789delGAG	X52425	CCDS10629.1, CCDS58441.1	16p12.1-p11.2	2008-05-14			ENSG00000077238	ENSG00000077238		"""Interleukins and interleukin receptors"", ""CD molecules"""	6015	protein-coding gene	gene with protein product		147781				1679753	Standard	NM_000418		Approved	CD124	uc010bxy.4	P24394	OTTHUMG00000097015	ENST00000395762.2:c.1114_1116delGAG	16.37:g.27373796_27373798delGAG	ENSP00000379111:p.Glu376del					IL4R_ENST00000170630.2_In_Frame_Del_p.E376del|IL4R_ENST00000543915.2_In_Frame_Del_p.E376del|IL4R_ENST00000380922.3_In_Frame_Del_p.E361del|IL4R_ENST00000565915.1_3'UTR	p.E376del	NM_000418.3	NP_000409.1	P24394	IL4RA_HUMAN			11	1373_1375	+			376			Poly-Glu.		B4E076|B9EKU8|H3BSY5|Q96P01|Q9H181|Q9H182|Q9H183|Q9H184|Q9H185|Q9H186|Q9H187|Q9H188	In_Frame_Del	DEL	ENST00000395762.2	37	c.1114_1116delGAG	CCDS10629.1																																																																																				0.591	IL4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214104.4			7	378						7	378	---	---	---	---
TAOK2	9344	broad.mit.edu	37	16	29998498	29998500	+	In_Frame_Del	DEL	CTG	CTG	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr16:29998498_29998500delCTG	ENST00000308893.4	+	16	3948_3950	c.2905_2907delCTG	c.(2905-2907)ctgdel	p.L974del	TAOK2_ENST00000416441.2_In_Frame_Del_p.L801del|TAOK2_ENST00000279394.3_Intron|TAOK2_ENST00000543033.1_In_Frame_Del_p.L861del	NM_001252043.1|NM_016151.3	NP_001238972.1|NP_057235.2	Q9UL54	TAOK2_HUMAN	TAO kinase 2	974	Leu-rich.				actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|cell migration (GO:0016477)|cellular response to DNA damage stimulus (GO:0006974)|focal adhesion assembly (GO:0048041)|G2 DNA damage checkpoint (GO:0031572)|positive regulation of JNK cascade (GO:0046330)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein targeting to membrane (GO:0006612)|regulation of cell growth (GO:0001558)|regulation of cell shape (GO:0008360)|response to stress (GO:0006950)|stress-activated MAPK cascade (GO:0051403)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleolus (GO:0005730)|nucleus (GO:0005634)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|mitogen-activated protein kinase kinase binding (GO:0031434)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(3)|skin(1)	22						CCTGCCCCTCCTGCTGCTGCTGC	0.709																																						ENST00000308893.4																			0				breast(1)|endometrium(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(3)|skin(1)	22						c.(2905-2907)del		TAO kinase 2			,	25,3845		3,19,1913					,	-6.7	0.0			32	41,7581		7,27,3777	no	coding,intron	TAOK2	NM_016151.2,NM_004783.2	,	10,46,5690	A1A1,A1R,RR		0.5379,0.646,0.5743	,	,		66,11426				SO:0001651	inframe_deletion	9344				actin cytoskeleton organization|activation of MAPKK activity|apoptosis|cell migration|focal adhesion assembly|positive regulation of JNK cascade|protein targeting to membrane|regulation of cell growth|regulation of cell shape|response to stress	cytoplasmic vesicle membrane|cytoskeleton|dendrite|integral to membrane|nucleolus	ATP binding|protein serine/threonine kinase activity	g.chr16:29998498_29998500delCTG	AB020688	CCDS10662.1, CCDS10663.1, CCDS58448.1	16p11.2	2008-02-05			ENSG00000149930	ENSG00000149930			16835	protein-coding gene	gene with protein product		613199				10048485, 9786855	Standard	NM_016151		Approved	TAO1, KIAA0881, PSK, PSK1, TAO2, MAP3K17	uc002dva.2	Q9UL54	OTTHUMG00000132111	ENST00000308893.4:c.2905_2907delCTG	16.37:g.29998507_29998509delCTG	ENSP00000310094:p.Leu974del					TAOK2_ENST00000543033.1_In_Frame_Del_p.L861del|TAOK2_ENST00000279394.3_Intron|TAOK2_ENST00000416441.2_In_Frame_Del_p.L801del	p.L974del	NM_001252043.1|NM_016151.3	NP_001238972.1|NP_057235.2	Q9UL54	TAOK2_HUMAN			16	3948_3950	+			974			Leu-rich.		A5PKY1|A7MCZ2|B2RN35|B7ZM88|O94957|Q6UW73|Q7LC09|Q9NSW2	In_Frame_Del	DEL	ENST00000308893.4	37	c.2905_2907delCTG	CCDS10663.1																																																																																				0.709	TAOK2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255152.2	NM_016151		7	592						7	592	---	---	---	---
BCL7C	9274	broad.mit.edu	37	16	30899223	30899223	+	Frame_Shift_Del	DEL	G	G	-	rs150838242		TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr16:30899223delG	ENST00000215115.4	-	6	1632	c.617delC	c.(616-618)ccafs	p.P206fs	MIR4519_ENST00000570025.1_RNA|MIR4519_ENST00000565573.1_RNA|BCL7C_ENST00000380317.4_Intron|MIR4519_ENST00000564901.1_RNA|AC106782.20_ENST00000572471.1_RNA	NM_004765.2	NP_004756.2	Q8WUZ0	BCL7C_HUMAN	B-cell CLL/lymphoma 7C	206	Pro-rich.				apoptotic process (GO:0006915)					large_intestine(1)|lung(3)|prostate(1)|skin(1)	6			Colorectal(24;0.198)			GCGCTTGAGTGGGGGGGCACC	0.622																																						ENST00000215115.4																			0				large_intestine(1)|lung(3)|prostate(1)|skin(1)	6						c.(616-618)cafs		B-cell CLL/lymphoma 7C							76.0	92.0	87.0					16																	30899223		2197	4300	6497	SO:0001589	frameshift_variant	9274				apoptosis			g.chr16:30899223delG	AJ223980	CCDS10693.1, CCDS67012.1	16p11	2012-11-19			ENSG00000099385	ENSG00000099385			1006	protein-coding gene	gene with protein product		605847				9931421	Standard	NM_004765		Approved		uc002dzv.3	Q8WUZ0	OTTHUMG00000177719	ENST00000215115.4:c.617delC	16.37:g.30899223delG	ENSP00000215115:p.Pro206fs					MIR4519_ENST00000565573.1_RNA|BCL7C_ENST00000380317.4_Intron|MIR4519_ENST00000564901.1_RNA|AC106782.20_ENST00000572471.1_RNA|MIR4519_ENST00000570025.1_RNA	p.P206fs	NM_004765.2	NP_004756.2	Q8WUZ0	BCL7C_HUMAN	Colorectal(24;0.198)		6	1632	-			206			Pro-rich.		O43770|Q6PD89	Frame_Shift_Del	DEL	ENST00000215115.4	37	c.617delC	CCDS10693.1																																																																																				0.622	BCL7C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255547.3	NM_004765		8	1315						8	1315	---	---	---	---
RP11-439I14.2	0	broad.mit.edu	37	16	64770704	64770705	+	lincRNA	INS	-	-	CCAGTGATGGTCACCT	rs200421189|rs71143515|rs377231404|rs145408521|rs140029302	byFrequency	TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr16:64770704_64770705insCCAGTGATGGTCACCT	ENST00000564293.1	+	0	453_454																											TGTCACCACTGCCACCTTGTTC	0.371														3288	0.65655	0.8434	0.5144	5008	,	,		21531	0.6052		0.5537	False		,,,				2504	0.6636					ENST00000564293.1																			0																																																			0							g.chr16:64770704_64770705insCCAGTGATGGTCACCT																													16.37:g.64770704_64770705insCCAGTGATGGTCACCT														0	453_454	+									RNA	INS	ENST00000564293.1	37																																																																																						0.371	RP11-439I14.2-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000422725.1			9	39						9	39	---	---	---	---
NFAT5	10725	broad.mit.edu	37	16	69726420	69726422	+	In_Frame_Del	DEL	CAG	CAG	-	rs369235958		TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr16:69726420_69726422delCAG	ENST00000354436.2	+	12	2956_2958	c.2638_2640delCAG	c.(2638-2640)cagdel	p.Q888del	NFAT5_ENST00000349945.1_In_Frame_Del_p.Q812del|NFAT5_ENST00000567239.1_In_Frame_Del_p.Q905del|NFAT5_ENST00000566899.1_In_Frame_Del_p.Q812del|NFAT5_ENST00000432919.1_In_Frame_Del_p.Q906del|NFAT5_ENST00000393742.2_In_Frame_Del_p.Q812del	NM_006599.3	NP_006590.1	O94916	NFAT5_HUMAN	nuclear factor of activated T-cells 5, tonicity-responsive	888	Poly-Gln.				cytokine production (GO:0001816)|excretion (GO:0007588)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of calcineurin-NFAT signaling cascade (GO:0070884)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Q804Q(1)|p.Q898Q(1)		NS(1)|breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(11)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						ATCTAATcaacagcagcagcagc	0.473																																						ENST00000349945.1																			2	Substitution - coding silent(2)	p.Q804Q(1)|p.Q898Q(1)	endometrium(2)	NS(1)|breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(11)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						c.(2410-2412)del		nuclear factor of activated T-cells 5, tonicity-responsive																																				SO:0001651	inframe_deletion	10725				excretion|signal transduction|transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity	g.chr16:69726420_69726422delCAG	AF134870	CCDS10881.1, CCDS10882.1, CCDS45519.1	16q22.1	2009-11-24			ENSG00000102908	ENSG00000102908		"""Nuclear factor of activated T-cells"""	7774	protein-coding gene	gene with protein product		604708				10377394	Standard	NM_173214		Approved	TONEBP, KIAA0827, NFATL1, OREBP, NFATZ, NF-AT5	uc002exl.2	O94916	OTTHUMG00000137572	ENST00000354436.2:c.2638_2640delCAG	16.37:g.69726429_69726431delCAG	ENSP00000346420:p.Gln888del					NFAT5_ENST00000432919.1_In_Frame_Del_p.Q906del|NFAT5_ENST00000567239.1_In_Frame_Del_p.Q905del|NFAT5_ENST00000354436.2_In_Frame_Del_p.Q888del|NFAT5_ENST00000566899.1_In_Frame_Del_p.Q812del|NFAT5_ENST00000393742.2_In_Frame_Del_p.Q812del	p.Q812del	NM_138714.3	NP_619728.2	O94916	NFAT5_HUMAN			14	3962_3964	+			888					A2RRB4|A6H8V5|E9PHR7|O95693|Q7LA65|Q969Q8|Q96QH3|Q9UN18	In_Frame_Del	DEL	ENST00000354436.2	37	c.2410_2412delCAG	CCDS10881.1																																																																																				0.473	NFAT5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268952.2	NM_138714		13	342						13	342	---	---	---	---
RP5-991G20.1	0	broad.mit.edu	37	16	72763869	72763869	+	RNA	DEL	A	A	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	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			9	34						9	34	---	---	---	---
ZFHX3	463	broad.mit.edu	37	16	72991713	72991715	+	In_Frame_Del	DEL	CCA	CCA	-	rs4788682	byFrequency	TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr16:72991713_72991715delCCA	ENST00000268489.5	-	2	3002_3004	c.2330_2332delTGG	c.(2329-2334)gtggct>gct	p.V777del	ZFHX3_ENST00000397992.5_Intron	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	777	Poly-Ala.		V -> A (in dbSNP:rs4788682). {ECO:0000269|PubMed:7592926}.		brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.V777V(1)		NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				gccgccgcagccaccgccgccgc	0.635																																						ENST00000268489.5																			1	Substitution - coding silent(1)	p.V777V(1)	lung(1)	NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153						c.(2329-2334)gct>g		zinc finger homeobox 3			,	1706,1886		582,542,672					,	5.5	0.1			17	4240,2792		1606,1028,882	no	coding,intron	ZFHX3	NM_006885.3,NM_001164766.1	,	2188,1570,1554	A1A1,A1R,RR		39.7042,47.4944,44.0324	,	,		5946,4678				SO:0001651	inframe_deletion	463				muscle organ development|negative regulation of myoblast differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|positive regulation of myoblast differentiation	transcription factor complex	enzyme binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription regulatory region DNA binding|zinc ion binding	g.chr16:72991713_72991715delCCA	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	777	protein-coding gene	gene with protein product		104155	"""AT-binding transcription factor 1"""	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.2330_2332delTGG	16.37:g.72991713_72991715delCCA	ENSP00000268489:p.Val777del					ZFHX3_ENST00000397992.5_Intron	p.VA777del	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN			2	3002_3004	-		Ovarian(137;0.13)	777		V -> A (in dbSNP:rs4788682).	Poly-Ala.		D3DWS8|O15101|Q13719	In_Frame_Del	DEL	ENST00000268489.5	37	c.2330_2332delTGG	CCDS10908.1																																																																																				0.635	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885		14	543						14	543	---	---	---	---
NPIPB15	440348	broad.mit.edu	37	16	74425400	74425402	+	In_Frame_Del	DEL	CAA	CAA	-	rs370078939		TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr16:74425400_74425402delCAA	ENST00000429990.1	+	7	850_852	c.754_756delCAA	c.(754-756)caadel	p.Q253del				A6NHN6	NPB15_HUMAN	nuclear pore complex interacting protein family, member B15	253	Pro-rich.					extracellular region (GO:0005576)											TCCTCCAACTCAACAACATTCTA	0.517																																						ENST00000429990.1																			0											c.(754-756)del		nuclear pore complex interacting protein family, member B15																																				SO:0001651	inframe_deletion	440348							g.chr16:74425400_74425402delCAA	BC160029		16q22.3	2013-06-11	2013-06-11	2013-06-11	ENSG00000196436	ENSG00000196436			34409	protein-coding gene	gene with protein product			"""nuclear pore complex interacting protein-like 2"""	NPIPL2			Standard	XM_005256273		Approved	LOC440348	uc010vmt.1	A6NHN6	OTTHUMG00000156916	ENST00000429990.1:c.754_756delCAA	16.37:g.74425403_74425405delCAA	ENSP00000411140:p.Gln253del						p.Q253del							7	850_852	+								C9J9U8	In_Frame_Del	DEL	ENST00000429990.1	37	c.754_756delCAA																																																																																					0.517	NPIPB15-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000346597.2	NM_001018059		10	426						10	426	---	---	---	---
TCF25	22980	broad.mit.edu	37	16	89951019	89951020	+	Frame_Shift_Ins	INS	-	-	A			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr16:89951019_89951020insA	ENST00000263346.8	+	3	440_441	c.384_385insA	c.(385-387)aaafs	p.K129fs	TCF25_ENST00000263347.7_5'Flank|TCF25_ENST00000563406.1_3'UTR	NM_014972.2	NP_055787.1	Q9BQ70	TCF25_HUMAN	transcription factor 25 (basic helix-loop-helix)	129					heart development (GO:0007507)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|large_intestine(1)|lung(8)|ovary(3)|skin(1)|urinary_tract(2)	18		all_cancers(9;4.71e-08)|Lung NSC(15;0.000192)|all_lung(18;0.000319)|all_neural(9;0.0122)|all_hematologic(23;0.027)		BRCA - Breast invasive adenocarcinoma(80;0.0288)		TCCGGAAGAAGAAAAAAAAACA	0.446																																						ENST00000263346.8																			0				breast(1)|endometrium(2)|large_intestine(1)|lung(8)|ovary(3)|skin(1)|urinary_tract(2)	18						c.(382-387)aaaaaafs		transcription factor 25 (basic helix-loop-helix)																																				SO:0001589	frameshift_variant	22980				heart development|negative regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity	g.chr16:89951019_89951020insA	AF322111	CCDS10987.1	16q24.3	2008-02-05			ENSG00000141002	ENSG00000141002			29181	protein-coding gene	gene with protein product		612326				12107429, 16574069	Standard	NM_014972		Approved	Nulp1, KIAA1049	uc002fpb.2	Q9BQ70	OTTHUMG00000138986	ENST00000263346.8:c.393dupA	16.37:g.89951028_89951028dupA	ENSP00000263346:p.Lys129fs					TCF25_ENST00000563406.1_3'UTR	p.KK128fs	NM_014972.2	NP_055787.1	Q9BQ70	TCF25_HUMAN		BRCA - Breast invasive adenocarcinoma(80;0.0288)	3	440_441	+		all_cancers(9;4.71e-08)|Lung NSC(15;0.000192)|all_lung(18;0.000319)|all_neural(9;0.0122)|all_hematologic(23;0.027)	128					Q2MK75|Q9UPV3	Frame_Shift_Ins	INS	ENST00000263346.8	37	c.384_385insA	CCDS10987.1																																																																																				0.446	TCF25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272875.2	NM_014972		9	194						9	194	---	---	---	---
ITGAE	3682	broad.mit.edu	37	17	3664312	3664314	+	In_Frame_Del	DEL	TCC	TCC	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr17:3664312_3664314delTCC	ENST00000263087.4	-	6	689_691	c.591_593delGGA	c.(589-594)gaggaa>gaa	p.197_198EE>E		NM_002208.4	NP_002199.3	P38570	ITAE_HUMAN	integrin, alpha E (antigen CD103, human mucosal lymphocyte antigen 1; alpha polypeptide)	197	Glu-rich (acidic).|X-domain (extra domain).				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)	external side of plasma membrane (GO:0009897)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			NS(1)|breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	41				UCEC - Uterine corpus endometrioid carcinoma (3;0.0813)		CTCACCAGCTtcctcctcctcct	0.586																																					NSCLC(182;635 2928 8995 38788)	ENST00000263087.4																			0				NS(1)|breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	41						c.(589-594)gaa>ga		integrin, alpha E (antigen CD103, human mucosal lymphocyte antigen 1; alpha polypeptide)																																				SO:0001651	inframe_deletion	3682				cell adhesion|integrin-mediated signaling pathway	integrin complex	receptor activity	g.chr17:3664312_3664314delTCC	L25851	CCDS32531.1	17p13	2010-03-23				ENSG00000083457		"""CD molecules"", ""Integrins"""	6147	protein-coding gene	gene with protein product		604682				8119947	Standard	NM_002208		Approved	CD103, HUMINAE	uc002fwo.4	P38570		ENST00000263087.4:c.591_593delGGA	17.37:g.3664321_3664323delTCC	ENSP00000263087:p.Glu198del						p.EE197del	NM_002208.4	NP_002199.3	P38570	ITAE_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (3;0.0813)	6	689_691	-			197			Glu-rich (acidic).|X-domain (extra domain).		Q17RS6|Q9NZU9	In_Frame_Del	DEL	ENST00000263087.4	37	c.591_593delGGA	CCDS32531.1																																																																																				0.586	ITGAE-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438169.1	NM_002208		7	569						7	569	---	---	---	---
NLRP1	22861	broad.mit.edu	37	17	5463340	5463341	+	Frame_Shift_Del	DEL	TC	TC	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr17:5463340_5463341delTC	ENST00000572272.1	-	4	674_675	c.675_676delGA	c.(673-678)gagaaafs	p.K226fs	NLRP1_ENST00000269280.4_Frame_Shift_Del_p.K226fs|NLRP1_ENST00000354411.3_Frame_Shift_Del_p.K226fs|NLRP1_ENST00000571307.1_5'UTR|NLRP1_ENST00000577119.1_Frame_Shift_Del_p.K226fs|NLRP1_ENST00000345221.3_Frame_Shift_Del_p.K226fs|NLRP1_ENST00000262467.5_Frame_Shift_Del_p.K226fs			Q9C000	NALP1_HUMAN	NLR family, pyrin domain containing 1	226					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|defense response to bacterium (GO:0042742)|innate immune response (GO:0045087)|neuron apoptotic process (GO:0051402)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of interleukin-1 beta secretion (GO:0050718)|regulation of inflammatory response (GO:0050727)|response to muramyl dipeptide (GO:0032495)	cytosol (GO:0005829)|intracellular (GO:0005622)|NLRP1 inflammasome complex (GO:0072558)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|enzyme binding (GO:0019899)|protein domain specific binding (GO:0019904)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(17)|liver(5)|lung(17)|ovary(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Colorectal(1115;3.48e-05)				TTCTCTGATTTCTCTCTCTCTC	0.48																																						ENST00000345221.3																			0				breast(4)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(17)|liver(5)|lung(17)|ovary(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						c.(673-678)gaaafs		NLR family, pyrin domain containing 1																																				SO:0001589	frameshift_variant	22861				defense response to bacterium|induction of apoptosis|neuron apoptosis|positive regulation of interleukin-1 beta secretion|response to muramyl dipeptide	cytoplasm|NALP1 inflammasome complex|nucleus	ATP binding|caspase activator activity|enzyme binding|protein domain specific binding	g.chr17:5463340_5463341delTC	AB023143	CCDS32537.1, CCDS42244.1, CCDS42245.1, CCDS42246.1, CCDS58508.1	17p13	2014-01-29	2006-12-08	2006-12-08	ENSG00000091592	ENSG00000091592		"""Nucleotide-binding domain and leucine rich repeat containing"""	14374	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 1"""	606636	"""NACHT, leucine rich repeat and PYD (pyrin domain) containing 1"", ""systemic lupus erythematosus, vitiligo-related 1"""	NALP1, SLEV1		8781126, 12563287, 17377159	Standard	NM_033006		Approved	KIAA0926, DKFZp586O1822, CARD7, NAC, CLR17.1, DEFCAP, VAMAS1	uc002gci.3	Q9C000		ENST00000572272.1:c.675_676delGA	17.37:g.5463350_5463351delTC	ENSP00000460475:p.Lys226fs					NLRP1_ENST00000571307.1_5'UTR|NLRP1_ENST00000354411.3_Frame_Shift_Del_p.EK225fs|NLRP1_ENST00000262467.5_Frame_Shift_Del_p.EK225fs|NLRP1_ENST00000572272.1_Frame_Shift_Del_p.EK225fs|NLRP1_ENST00000269280.4_Frame_Shift_Del_p.EK225fs|NLRP1_ENST00000577119.1_Frame_Shift_Del_p.EK225fs	p.EK225fs	NM_014922.4|NM_033004.3|NM_033007.3	NP_055737.1|NP_127497.1|NP_127500.1	Q9C000	NALP1_HUMAN			4	1229_1230	-		Colorectal(1115;3.48e-05)	225					E9PE50|I6L9D9|Q9BZZ8|Q9BZZ9|Q9H5Z7|Q9H5Z8|Q9HAV8|Q9UFT4|Q9Y2E0	Frame_Shift_Del	DEL	ENST00000572272.1	37	c.675_676delGA	CCDS42246.1																																																																																				0.480	NLRP1-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439517.1	NM_033004		8	394						8	394	---	---	---	---
TMEM199	147007	broad.mit.edu	37	17	26684394	26684395	+	5'Flank	INS	-	-	G	rs202089331|rs17856014	byFrequency	TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr17:26684394_26684395insG	ENST00000292114.3	+	0	0				POLDIP2_ENST00000540200.1_Splice_Site|CTB-96E2.3_ENST00000591482.1_RNA|TMEM199_ENST00000509083.1_5'Flank|TMEM199_ENST00000395404.3_5'Flank|POLDIP2_ENST00000003607.4_5'UTR	NM_152464.1	NP_689677.1	Q8N511	TM199_HUMAN	transmembrane protein 199							integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(1)|lung(2)	6	all_lung(13;0.000354)|Lung NSC(42;0.00115)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)		AGAGCGGCTTTGCCACCGGGCC	0.762																																						ENST00000540200.1																			0											c.e1+1		polymerase (DNA-directed), delta interacting protein 2				2770,50		1380,10,20						0.4	0.1		dbSNP_130	4	6440,112		3203,34,39	no	frameshift	POLDIP2	NM_015584.3		4583,44,59	A1A1,A1R,RR		1.7094,1.773,1.7286				9210,162				SO:0001631	upstream_gene_variant	26073					mitochondrial nucleoid|nucleus		g.chr17:26684394_26684395insG	AY074907	CCDS11228.1	17q11.2	2007-12-17	2007-12-17	2007-12-17	ENSG00000244045	ENSG00000244045			18085	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 32"""	C17orf32			Standard	NM_152464		Approved	MGC45714	uc002hba.3	Q8N511	OTTHUMG00000132498		17.37:g.26684395_26684395dupG	Exception_encountered					POLDIP2_ENST00000003607.4_5'UTR		NM_015584.3	NP_056399.1	Q9Y2S7	PDIP2_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (53;0.154)	1	78	-	all_lung(13;0.000354)|Lung NSC(42;0.00115)								Splice_Site	INS	ENST00000292114.3	37		CCDS11228.1																																																																																				0.762	TMEM199-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255676.2	NM_152464		8	25						8	25	---	---	---	---
NUFIP2	57532	broad.mit.edu	37	17	27620990	27620992	+	In_Frame_Del	DEL	GCT	GCT	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr17:27620990_27620992delGCT	ENST00000225388.4	-	1	144_146	c.86_88delAGC	c.(85-90)cagccg>ccg	p.Q29del	NUFIP2_ENST00000579665.1_In_Frame_Del_p.Q29del	NM_020772.2	NP_065823.1	Q7Z417	NUFP2_HUMAN	nuclear fragile X mental retardation protein interacting protein 2	29	His-rich.					cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)|polysomal ribosome (GO:0042788)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(1)|lung(7)|ovary(1)|prostate(2)|skin(4)|urinary_tract(1)	24			BRCA - Breast invasive adenocarcinoma(11;0.000457)|Colorectal(6;0.0178)|COAD - Colon adenocarcinoma(6;0.0551)			tggtggtgcggctgctgctgctg	0.591																																						ENST00000225388.4																			0				breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(1)|lung(7)|ovary(1)|prostate(2)|skin(4)|urinary_tract(1)	24						c.(85-90)ccg>c		nuclear fragile X mental retardation protein interacting protein 2																																				SO:0001651	inframe_deletion	57532					nucleus|polysomal ribosome	protein binding|RNA binding	g.chr17:27620990_27620992delGCT	AB037742	CCDS32600.1	17q11.1	2006-03-01				ENSG00000108256			17634	protein-coding gene	gene with protein product		609356				12837692, 16407062	Standard	NM_020772		Approved	KIAA1321, MGC117262, PIG1, 182-FIP, FIP-82, 82-FIP	uc002hdy.4	Q7Z417		ENST00000225388.4:c.86_88delAGC	17.37:g.27620999_27621001delGCT	ENSP00000225388:p.Gln29del					NUFIP2_ENST00000579665.1_In_Frame_Del_p.QP29del	p.QP29del	NM_020772.2	NP_065823.1	Q7Z417	NUFP2_HUMAN	BRCA - Breast invasive adenocarcinoma(11;0.000457)|Colorectal(6;0.0178)|COAD - Colon adenocarcinoma(6;0.0551)		1	144_146	-			29			His-rich.		A1L3A6|Q9P2M5	In_Frame_Del	DEL	ENST00000225388.4	37	c.86_88delAGC	CCDS32600.1																																																																																				0.591	NUFIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447015.2	NM_020772		16	466						16	466	---	---	---	---
ZNF207	7756	broad.mit.edu	37	17	30677314	30677316	+	In_Frame_Del	DEL	AAG	AAG	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr17:30677314_30677316delAAG	ENST00000321233.6	+	1	164_166	c.10_12delAAG	c.(10-12)aagdel	p.K7del	RP11-227G15.3_ENST00000581915.1_RNA|ZNF207_ENST00000342555.6_5'UTR|ZNF207_ENST00000341711.6_In_Frame_Del_p.K7del|MIR632_ENST00000385193.1_RNA|ZNF207_ENST00000577908.1_In_Frame_Del_p.K7del|ZNF207_ENST00000394673.2_In_Frame_Del_p.K7del|ZNF207_ENST00000394670.4_In_Frame_Del_p.K7del	NM_003457.3	NP_003448.1	O43670	ZN207_HUMAN	zinc finger protein 207	7	Microtubule-binding region.				attachment of spindle microtubules to kinetochore (GO:0008608)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle assembly checkpoint (GO:0007094)|protein stabilization (GO:0050821)|regulation of chromosome segregation (GO:0051983)|regulation of transcription, DNA-templated (GO:0006355)	kinetochore (GO:0000776)|microtubule (GO:0005874)|nucleus (GO:0005634)	DNA binding (GO:0003677)|heparin binding (GO:0008201)|microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(2)|lung(3)|urinary_tract(2)	10		Breast(31;0.116)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.239)			TATGGGTCGCAAGAAGAAGAAGC	0.542																																						ENST00000394670.4																			0				breast(1)|endometrium(2)|kidney(2)|lung(3)|urinary_tract(2)	10						c.(10-12)del		zinc finger protein 207																																				SO:0001651	inframe_deletion	7756					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding	g.chr17:30677314_30677316delAAG	AF046001	CCDS11271.1, CCDS32614.1, CCDS42294.1	17q11.2	2008-07-10			ENSG00000010244	ENSG00000010244		"""Zinc fingers, C2H2-type"""	12998	protein-coding gene	gene with protein product		603428				9799612	Standard	NM_001098507		Approved		uc002hhj.4	O43670	OTTHUMG00000132810	ENST00000321233.6:c.10_12delAAG	17.37:g.30677323_30677325delAAG	ENSP00000322777:p.Lys7del					RP11-227G15.3_ENST00000581915.1_RNA|ZNF207_ENST00000341711.6_In_Frame_Del_p.K7del|ZNF207_ENST00000321233.6_In_Frame_Del_p.K7del|ZNF207_ENST00000577908.1_In_Frame_Del_p.K7del|ZNF207_ENST00000394673.2_In_Frame_Del_p.K7del|ZNF207_ENST00000342555.6_5'UTR	p.K7del	NM_001098507.1	NP_001091977.1	O43670	ZN207_HUMAN	BRCA - Breast invasive adenocarcinoma(9;0.239)		1	179_181	+		Breast(31;0.116)|Ovarian(249;0.182)	7					A8K6Y6|E1P660|E1P661|E1P662|Q53XS9|Q96HW5|Q9BUQ7	In_Frame_Del	DEL	ENST00000321233.6	37	c.10_12delAAG	CCDS11271.1																																																																																				0.542	ZNF207-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256251.2			8	1172						8	1172	---	---	---	---
KRTAP4-1	85285	broad.mit.edu	37	17	39340796	39340852	+	In_Frame_Del	DEL	CGGCAGCAGCTGGACATACCACAGCTGGGGTGGCAGGTGGTCTGACAGCAGAGTGGG	CGGCAGCAGCTGGACATACCACAGCTGGGGTGGCAGGTGGTCTGACAGCAGAGTGGG	-	rs483929|rs543483191|rs79048996|rs1985673|rs2320229|rs483893|rs572749|rs543006020|rs71155126|rs554407371|rs2320230	byFrequency	TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr17:39340796_39340852delCGGCAGCAGCTGGACATACCACAGCTGGGGTGGCAGGTGGTCTGACAGCAGAGTGGG	ENST00000398472.1	-	1	742_798	c.255_311delCCCACTCTGCTGTCAGACCACCTGCCACCCCAGCTGTGGTATGTCCAGCTGCTGCCG	c.(253-312)cgcccactctgctgtcagaccacctgccaccccagctgtggtatgtccagctgctgccgt>cgt	p.85_104RPLCCQTTCHPSCGMSSCCR>R				Q9BYQ7	KRA41_HUMAN	keratin associated protein 4-1	85	18 X 5 AA repeats of C-C-[GRQC]-[SPT]- [VSTL].		Missing (in allele KAP4.10). {ECO:0000269|PubMed:15955084}.			keratin filament (GO:0045095)		p.H90_C108delHPSCGMSSCCRPLCCQTTC(2)|p.H94_C112delHPSCGMSSCCRPLCCQTTC(2)		kidney(1)|large_intestine(1)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	5		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			ACAGAGTGGACGGCAGCAGCTGGACATACCACAGCTGGGGTGGCAGGTGGTCTGACAGCAGAGTGGGCGGCAGCAGC	0.646																																						ENST00000398472.1																			4	Deletion - In frame(4)	p.H90_C108delHPSCGMSSCCRPLCCQTTC(2)|p.H94_C112delHPSCGMSSCCRPLCCQTTC(2)	upper_aerodigestive_tract(2)|prostate(2)	kidney(1)|large_intestine(1)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	5						c.(253-312)cgt>cg		keratin associated protein 4-1																																				SO:0001651	inframe_deletion	85285					keratin filament		g.chr17:39340796_39340852delCGGCAGCAGCTGGACATACCACAGCTGGGGTGGCAGGTGGTCTGACAGCAGAGTGGG	AC006070		17q21.2	2013-06-25			ENSG00000198443	ENSG00000198443		"""Keratin associated proteins"""	18907	protein-coding gene	gene with protein product			"""keratin associated protein 4-10"""	KRTAP4-10		11279113	Standard	NM_033060		Approved	KAP4.1, KAP4.10	uc002hwe.4	Q9BYQ7	OTTHUMG00000132081	ENST00000398472.1:c.255_311delCCCACTCTGCTGTCAGACCACCTGCCACCCCAGCTGTGGTATGTCCAGCTGCTGCCG	17.37:g.39340796_39340852delCGGCAGCAGCTGGACATACCACAGCTGGGGTGGCAGGTGGTCTGACAGCAGAGTGGG	ENSP00000381489:p.Arg85_Cys103del						p.RPLCCQTTCHPSCGMSSCCR85del			Q9BYQ7	KRA41_HUMAN	STAD - Stomach adenocarcinoma(17;0.000449)		1	742_798	-		Breast(137;0.000496)	85		Missing (in allele KAP4.10).	18 X 5 AA repeats of C-C-[GRQC]-[SPT]- [VSTL].		A8MWS7|Q3SYF2	In_Frame_Del	DEL	ENST00000398472.1	37	c.255_311delCCCACTCTGCTGTCAGACCACCTGCCACCCCAGCTGTGGTATGTCCAGCTGCTGCCG																																																																																					0.646	KRTAP4-1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255108.1	NM_033060		14	403						14	403	---	---	---	---
BZRAP1	9256	broad.mit.edu	37	17	56387404	56387406	+	In_Frame_Del	DEL	TCC	TCC	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr17:56387404_56387406delTCC	ENST00000343736.4	-	21	3976_3978	c.3813_3815delGGA	c.(3811-3816)gaggaa>gaa	p.1271_1272EE>E	BZRAP1_ENST00000268893.6_In_Frame_Del_p.1211_1212EE>E|BZRAP1_ENST00000355701.3_In_Frame_Del_p.1271_1272EE>E			O95153	RIMB1_HUMAN	benzodiazepine receptor (peripheral) associated protein 1	1271	Poly-Glu.					cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	benzodiazepine receptor binding (GO:0030156)			cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	Medulloblastoma(34;0.127)|all_neural(34;0.237)					CAGctcctcttcctcctcctcct	0.586																																						ENST00000355701.3																			0				cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	54						c.(3811-3816)gaa>ga		benzodiazapine receptor (peripheral) associated protein 1			,	10,0,4254		4,0,2,0,0,2126					,	-7.0	0.1			91	24,2,8228		10,0,4,0,2,4111	no	codingComplex,codingComplex	BZRAP1	NM_024418.1,NM_004758.2	,	14,0,6,0,2,6237	A1A1,A1A2,A1R,A2A2,A2R,RR		0.315,0.2345,0.2876	,	,		34,2,12482				SO:0001651	inframe_deletion	9256					mitochondrion	benzodiazepine receptor binding	g.chr17:56387404_56387406delTCC	AB014512	CCDS11605.1, CCDS45742.1	17q22-q23	2014-01-09	2014-01-09						16831	protein-coding gene	gene with protein product		610764				9734811, 9915832	Standard	NM_004758		Approved	PRAX-1, KIAA0612, RIM-BP1, RIMBP1	uc002ivx.5	O95153		ENST00000343736.4:c.3813_3815delGGA	17.37:g.56387413_56387415delTCC	ENSP00000345824:p.Glu1274del					BZRAP1_ENST00000343736.4_In_Frame_Del_p.EE1273del|BZRAP1_ENST00000268893.6_In_Frame_Del_p.EE1213del	p.EE1273del	NM_001261835.1|NM_004758.3	NP_001248764.1|NP_004749.2	O95153	RIMB1_HUMAN			21	4683_4685	-	Medulloblastoma(34;0.127)|all_neural(34;0.237)		1273			Poly-Glu.		O75111|Q8N5W3	In_Frame_Del	DEL	ENST00000343736.4	37	c.3813_3815delGGA	CCDS11605.1																																																																																				0.586	BZRAP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443980.1	NM_004758		8	459						8	459	---	---	---	---
ROCK1P1	727758	broad.mit.edu	37	18	112482	112482	+	RNA	DEL	C	C	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr18:112482delC	ENST00000608049.1	+	0	389					NR_033770.1				Rho-associated, coiled-coil containing protein kinase 1 pseudogene 1																		AGGGGTGCTTCCAGCGAGGCG	0.622																																						ENST00000576266.1																			0																																																			0							g.chr18:112482delC			18p11.32	2012-10-04			ENSG00000263006	ENSG00000263006			37832	pseudogene	pseudogene							Standard	NR_033770		Approved		uc002kke.3		OTTHUMG00000177913		18.37:g.112482delC														0	116	+									RNA	DEL	ENST00000608049.1	37																																																																																						0.622	ROCK1P1-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000472417.1			11	173						11	173	---	---	---	---
SNORA70	26778	broad.mit.edu	37	18	3025533	3025533	+	RNA	DEL	A	A	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr18:3025533delA	ENST00000516449.1	-	0	31									small nucleolar RNA, H/ACA box 70																		ACAACTTCTTAAAAAAAAAAt	0.473																																						ENST00000516449.1																			0																																																			0							g.chr18:3025533delA	Y11164		Xq28	2013-09-05	2006-04-05	2006-04-05	ENSG00000207165	ENSG00000207165		"""ncRNAs / Small nucleolar RNAs : H/ACA box containing"""	10231	non-coding RNA	RNA, small nucleolar			"""RNA, U70 small nucleolar"""	RNU70		9106664, 15199136	Standard	NR_000011		Approved	U70, DXS648E	uc021raw.1				18.37:g.3025533delA														0	31	-									RNA	DEL	ENST00000516449.1	37																																																																																						0.473	SNORA70.21-201	NOVEL	basic	snoRNA	snoRNA		NR_000011		9	151						9	151	---	---	---	---
SEH1L	81929	broad.mit.edu	37	18	12986927	12986929	+	3'UTR	DEL	TCC	TCC	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr18:12986927_12986929delTCC	ENST00000262124.11	+	0	2886_2888				SEH1L_ENST00000399892.2_In_Frame_Del_p.P385del|RP11-773H22.4_ENST00000588211.1_RNA	NM_031216.3	NP_112493.2	Q96EE3	SEH1_HUMAN	SEH1-like (S. cerevisiae)						attachment of spindle microtubules to kinetochore involved in mitotic sister chromatid segregation (GO:0051315)|carbohydrate metabolic process (GO:0005975)|cytokine production involved in inflammatory response (GO:0002534)|cytokine-mediated signaling pathway (GO:0019221)|defense response to Gram-positive bacterium (GO:0050830)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic metaphase plate congression (GO:0007080)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore organization (GO:0006999)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nuclear envelope (GO:0005635)|nuclear pore outer ring (GO:0031080)				central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(5)|pancreas(1)|prostate(1)	11						CCCAGCTCCTtcctcctcctcct	0.522																																						ENST00000399892.2																			0				central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(5)|pancreas(1)|prostate(1)	11						c.(1135-1140)ctt>ct		SEH1-like (S. cerevisiae)																																				SO:0001624	3_prime_UTR_variant	81929				attachment of spindle microtubules to kinetochore involved in mitotic sister chromatid segregation|carbohydrate metabolic process|cell division|glucose transport|mitotic metaphase plate congression|mitotic prometaphase|mRNA transport|nuclear pore organization|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|Nup107-160 complex		g.chr18:12986927_12986929delTCC	BC012430	CCDS32791.1, CCDS45832.1	18p11.21	2013-01-10				ENSG00000085415		"""WD repeat domain containing"""	30379	protein-coding gene	gene with protein product	"""sec13 like protein"", ""nucleoporin Seh1"""	609263				12196509, 14517296	Standard	XM_005258152		Approved	SEH1A, SEH1B, Seh1, SEC13L	uc002krq.3	Q96EE3		ENST00000262124.11:c.*1678TCC>-	18.37:g.12986936_12986938delTCC						SEH1L_ENST00000262124.11_3'UTR|RP11-773H22.4_ENST00000588211.1_RNA	p.LP379del	NM_001013437.1	NP_001013455.1	Q96EE3	SEH1_HUMAN			9	1238_1240	+			0					A8K5B1|Q8NFU6|Q96MH3|Q9C069	In_Frame_Del	DEL	ENST00000262124.11	37	c.1137_1139delTCC	CCDS45832.1																																																																																				0.522	SEH1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458254.1	NM_031216		7	263						7	263	---	---	---	---
CXXC1	30827	broad.mit.edu	37	18	47812275	47812277	+	In_Frame_Del	DEL	CTG	CTG	-	rs527645784	byFrequency	TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr18:47812275_47812277delCTG	ENST00000285106.6	-	5	1195_1197	c.481_483delCAG	c.(481-483)cagdel	p.Q161del	CXXC1_ENST00000589940.1_In_Frame_Del_p.Q161del|CXXC1_ENST00000412036.2_In_Frame_Del_p.Q161del|CXXC1_ENST00000587396.1_5'Flank	NM_001101654.1|NM_014593.3	NP_001095124.1|NP_055408.2	Q9P0U4	CXXC1_HUMAN	CXXC finger protein 1	161					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|histone H3-K4 methylation (GO:0051568)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	24						ACCGTTTGATctgctgctgctgc	0.557														27	0.00539137	0.0151	0.0	5008	,	,		19878	0.0		0.0	False		,,,				2504	0.0072					ENST00000285106.6																			0				autonomic_ganglia(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	24						c.(481-483)del		CXXC finger protein 1																																				SO:0001651	inframe_deletion	30827				histone H3-K4 methylation|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear speck|Set1C/COMPASS complex	protein binding|unmethylated CpG binding|zinc ion binding	g.chr18:47812275_47812277delCTG	BC014940	CCDS11945.1, CCDS45866.1	18q12	2014-02-20	2014-02-20		ENSG00000154832	ENSG00000154832		"""Zinc fingers, PHD-type"""	24343	protein-coding gene	gene with protein product	"""CpG binding protein"", ""DNA-binding protein with PHD finger and CXXC domain"", ""zinc finger, CpG binding-type containing 1"""	609150	"""CXXC finger 1 (PHD domain)"""			10799292, 10688657	Standard	NM_014593		Approved	HsT2645, PCCX1, hCGBP, PHF18, CGBP, SPP1, CFP1, ZCGPC1	uc002ler.4	Q9P0U4	OTTHUMG00000132670	ENST00000285106.6:c.481_483delCAG	18.37:g.47812284_47812286delCTG	ENSP00000285106:p.Gln161del					CXXC1_ENST00000412036.2_In_Frame_Del_p.Q161del|CXXC1_ENST00000589940.1_In_Frame_Del_p.Q161del	p.Q161del	NM_001101654.1|NM_014593.3	NP_001095124.1|NP_055408.2	Q9P0U4	CXXC1_HUMAN			5	1195_1197	-			161					B2RC03|Q8N2W4|Q96BC8|Q9P2V7	In_Frame_Del	DEL	ENST00000285106.6	37	c.481_483delCAG	CCDS11945.1																																																																																				0.557	CXXC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255927.2	NM_014593		8	286						8	286	---	---	---	---
CDH19	28513	broad.mit.edu	37	18	64178924	64178925	+	Splice_Site	INS	-	-	A			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr18:64178924_64178925insA	ENST00000262150.2	-	10	1751		c.e10-2		CDH19_ENST00000540086.1_Intron	NM_021153.3	NP_066976.1	Q96JQ0	PCD16_HUMAN	cadherin 19, type 2						branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(22)|ovary(1)|prostate(3)|skin(7)	61		Esophageal squamous(42;0.0132)				CTGAATTACCTAAAAAAAAAGG	0.317																																						ENST00000262150.2																			0				NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(22)|ovary(1)|prostate(3)|skin(7)	61						c.e10-2		cadherin 19, type 2				8,4256		0,8,2124						4.9	1.0			66	12,8234		0,12,4111	no	splice-3	CDH19	NM_021153.2		0,20,6235	A1A1,A1R,RR		0.1455,0.1876,0.1599				20,12490				SO:0001630	splice_region_variant	28513				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding	g.chr18:64178924_64178925insA	AJ007607	CCDS11994.1, CCDS59325.1	18q22.1	2010-01-26			ENSG00000071991	ENSG00000071991		"""Cadherins / Major cadherins"""	1758	protein-coding gene	gene with protein product		603016				10995570	Standard	NM_021153		Approved	CDH7	uc002lkc.2	Q9H159	OTTHUMG00000132802	ENST00000262150.2:c.1459-2->T	18.37:g.64178933_64178933dupA						CDH19_ENST00000540086.1_Intron		NM_021153.2	NP_066976.1	Q9H159	CAD19_HUMAN			10	1751	-		Esophageal squamous(42;0.0132)						O15098	Splice_Site	INS	ENST00000262150.2	37		CCDS11994.1																																																																																				0.317	CDH19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256219.1	NM_021153	Intron	10	357						10	357	---	---	---	---
ZNF236	7776	broad.mit.edu	37	18	74593429	74593430	+	Frame_Shift_Ins	INS	-	-	A	rs201842338		TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr18:74593429_74593430insA	ENST00000253159.8	+	9	1570_1571	c.1372_1373insA	c.(1372-1374)gaafs	p.E458fs	ZNF236_ENST00000320610.9_Frame_Shift_Ins_p.E460fs	NM_007345.3	NP_031371.3	Q9UL36	ZN236_HUMAN	zinc finger protein 236	458					cellular response to glucose stimulus (GO:0071333)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(43)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	94		Prostate(75;0.0405)|Esophageal squamous(42;0.129)|Melanoma(33;0.132)		OV - Ovarian serous cystadenocarcinoma(15;4.36e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0686)		GGATAAAAAAGAAAAAAAAATG	0.381																																						ENST00000253159.8																			0				NS(1)|breast(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(43)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	94						c.(1372-1374)aaafs		zinc finger protein 236																																				SO:0001589	frameshift_variant	7776				cellular response to glucose stimulus	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding	g.chr18:74593429_74593430insA	AF085243	CCDS42447.1	18q22-q23	2013-01-08				ENSG00000130856		"""Zinc fingers, C2H2-type"""	13028	protein-coding gene	gene with protein product		604760				10458916	Standard	NM_007345		Approved		uc002lmi.3	Q9UL36		ENST00000253159.8:c.1381dupA	18.37:g.74593438_74593438dupA	ENSP00000253159:p.Glu458fs					ZNF236_ENST00000320610.9_Frame_Shift_Ins_p.K460fs	p.K458fs	NM_007345.3	NP_031371.3	Q9UL36	ZN236_HUMAN		OV - Ovarian serous cystadenocarcinoma(15;4.36e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0686)	9	1570_1571	+		Prostate(75;0.0405)|Esophageal squamous(42;0.129)|Melanoma(33;0.132)	458					B2RTX9|Q9UL37	Frame_Shift_Ins	INS	ENST00000253159.8	37	c.1372_1373insA	CCDS42447.1																																																																																				0.381	ZNF236-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000445776.1			8	356						8	356	---	---	---	---
MLLT1	4298	broad.mit.edu	37	19	6222272	6222274	+	In_Frame_Del	DEL	AGG	AGG	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr19:6222272_6222274delAGG	ENST00000252674.7	-	6	1131_1133	c.968_970delCCT	c.(967-972)tccttc>ttc	p.S323del		NM_005934.3	NP_005925.2	Q03111	ENL_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 1	323	Poly-Ser.				negative regulation of protein kinase activity (GO:0006469)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)	DNA binding (GO:0003677)			endometrium(3)|kidney(3)|large_intestine(2)|lung(5)|prostate(2)|skin(2)	17						TTGTCCGAGAAGGAGGAGGAGGA	0.65			T	MLL	AL																																	ENST00000252674.7				Dom	yes		19	19p13.3	4298	T	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 1 (ENL)"""			L	MLL		AL		0				endometrium(3)|kidney(3)|large_intestine(2)|lung(5)|prostate(2)|skin(2)	17						c.(967-972)ttc>t		myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 1				15,4239		1,13,2113						2.5	0.9			35	38,8216		0,38,4089	no	coding	MLLT1	NM_005934.3		1,51,6202	A1A1,A1R,RR		0.4604,0.3526,0.4237				53,12455				SO:0001651	inframe_deletion	4298				regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleolus	DNA binding|protein binding	g.chr19:6222272_6222274delAGG		CCDS12160.1	19p13.3	2012-10-04	2001-11-28		ENSG00000130382	ENSG00000130382			7134	protein-coding gene	gene with protein product		159556	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 1"""				Standard	XM_005259561		Approved	ENL, LTG19, YEATS1	uc002mek.3	Q03111	OTTHUMG00000180757	ENST00000252674.7:c.968_970delCCT	19.37:g.6222281_6222283delAGG	ENSP00000252674:p.Ser323del						p.SF323del	NM_005934.3	NP_005925.2	Q03111	ENL_HUMAN			6	1131_1133	-			323			Poly-Ser.		Q14768	In_Frame_Del	DEL	ENST00000252674.7	37	c.968_970delCCT	CCDS12160.1																																																																																				0.650	MLLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452909.1	NM_005934		8	206						8	206	---	---	---	---
ZNF44	51710	broad.mit.edu	37	19	12384448	12384448	+	Frame_Shift_Del	DEL	A	A	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr19:12384448delA	ENST00000356109.5	-	5	884	c.766delT	c.(766-768)tggfs	p.W256fs	ZNF44_ENST00000355684.5_Frame_Shift_Del_p.W208fs	NM_001164276.1	NP_001157748.1	P15621	ZNF44_HUMAN	zinc finger protein 44	256					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			ovary(1)	1		Renal(1328;0.157)		GBM - Glioblastoma multiforme(1328;0.0164)|Lung(535;0.179)		AAACTGGGCCAAAAAAAGGCT	0.398																																						ENST00000356109.5																			0				ovary(1)	1						c.(766-768)ggfs		zinc finger protein 44							88.0	93.0	92.0					19																	12384448		2203	4300	6503	SO:0001589	frameshift_variant	51710				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|microtubule cytoskeleton|nucleus	DNA binding|protein binding|zinc ion binding	g.chr19:12384448delA	X52338	CCDS45988.1, CCDS54223.1	19p13.2	2013-01-08	2006-05-11		ENSG00000197857	ENSG00000197857		"""Zinc fingers, C2H2-type"", ""-"""	13110	protein-coding gene	gene with protein product		194542	"""zinc finger protein 58"", ""zinc finger protein 44 (KOX 7)"", ""zinc finger protein 55"""	ZNF58, ZNF55		1946370, 1505991	Standard	NM_016264		Approved	KOX7, ZNF504	uc010xmj.2	P15621	OTTHUMG00000156424	ENST00000356109.5:c.766delT	19.37:g.12384448delA	ENSP00000348419:p.Trp256fs					ZNF44_ENST00000355684.5_Frame_Shift_Del_p.W208fs	p.W256fs	NM_001164276.1	NP_001157748.1	P15621	ZNF44_HUMAN		GBM - Glioblastoma multiforme(1328;0.0164)|Lung(535;0.179)	5	884	-		Renal(1328;0.157)	256					B4DML9|B9EGJ5|B9ZVM2|P17018|Q9ULZ7	Frame_Shift_Del	DEL	ENST00000356109.5	37	c.766delT	CCDS54223.1																																																																																				0.398	ZNF44-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344132.1	NM_016264		7	737						7	737	---	---	---	---
CCDC130	81576	broad.mit.edu	37	19	13873132	13873134	+	In_Frame_Del	DEL	AGG	AGG	-	rs148655062		TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr19:13873132_13873134delAGG	ENST00000586600.1	+	10	1096_1098	c.593_595delAGG	c.(592-597)caggag>cag	p.E202del	CCDC130_ENST00000587019.1_3'UTR|CCDC130_ENST00000221554.8_In_Frame_Del_p.E202del|MRI1_ENST00000319545.8_5'Flank|MRI1_ENST00000040663.6_5'Flank			P13994	CC130_HUMAN	coiled-coil domain containing 130	202					response to virus (GO:0009615)					endometrium(2)|kidney(1)|large_intestine(3)|ovary(1)|skin(2)|urinary_tract(1)	10			OV - Ovarian serous cystadenocarcinoma(19;6.02e-23)|Epithelial(5;2.58e-18)			AAAGCCATCCAGGAGGAGGAGGA	0.586																																						ENST00000586600.1																			0				endometrium(2)|kidney(1)|large_intestine(3)|ovary(1)|skin(2)|urinary_tract(1)	10						c.(592-597)cag>c		coiled-coil domain containing 130																																				SO:0001651	inframe_deletion	81576				response to virus		protein binding	g.chr19:13873132_13873134delAGG	AF250306	CCDS12296.1	19p13.13	2008-02-05				ENSG00000104957			28118	protein-coding gene	gene with protein product						3203696	Standard	NM_030818		Approved	MGC10471	uc002mxc.1	P13994		ENST00000586600.1:c.593_595delAGG	19.37:g.13873141_13873143delAGG	ENSP00000465776:p.Glu202del					CCDC130_ENST00000587019.1_3'UTR|CCDC130_ENST00000221554.8_In_Frame_Del_p.QE198del	p.QE198del			P13994	CC130_HUMAN	OV - Ovarian serous cystadenocarcinoma(19;6.02e-23)|Epithelial(5;2.58e-18)		10	1096_1098	+			198					Q9BQ72	In_Frame_Del	DEL	ENST00000586600.1	37	c.593_595delAGG	CCDS12296.1																																																																																				0.586	CCDC130-001	KNOWN	alternative_5_UTR|upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453216.2	NM_030818		7	799						7	799	---	---	---	---
HAUS8	93323	broad.mit.edu	37	19	17160706	17160707	+	Frame_Shift_Del	DEL	GA	GA	-	rs532006952		TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr19:17160706_17160707delGA	ENST00000253669.5	-	11	1399_1400	c.1209_1210delTC	c.(1207-1212)tctcgtfs	p.R404fs	CTD-2528A14.3_ENST00000598893.1_RNA|HAUS8_ENST00000448593.2_Frame_Shift_Del_p.R403fs|HAUS8_ENST00000593360.1_Frame_Shift_Del_p.R343fs			Q9BT25	HAUS8_HUMAN	HAUS augmin-like complex, subunit 8	404					centrosome organization (GO:0051297)|mitotic nuclear division (GO:0007067)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|HAUS complex (GO:0070652)|microtubule (GO:0005874)				endometrium(1)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)	12						CTCCCTGAACGAGAGAGAGAGG	0.495																																						ENST00000593360.1																			0				endometrium(1)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)	12						c.(1024-1029)tcgtfs		HAUS augmin-like complex, subunit 8																																				SO:0001589	frameshift_variant	93323				cell division|centrosome organization|mitosis|spindle assembly	centrosome|HAUS complex|microtubule|spindle pole		g.chr19:17160706_17160707delGA	BC004398	CCDS32948.1, CCDS46009.1	19p13.11	2013-10-11	2009-04-20	2009-04-20	ENSG00000131351	ENSG00000131351		"""HAUS augmin-like complex subunits"""	30532	protein-coding gene	gene with protein product		613434	"""HEC1/NDC80 interacting, centrosome associated 1"""	HICE1		19427217	Standard	XM_005260154		Approved	MGC20533, NY-SAR-48	uc002nfe.3	Q9BT25		ENST00000253669.5:c.1209_1210delTC	19.37:g.17160714_17160715delGA	ENSP00000253669:p.Arg404fs					HAUS8_ENST00000448593.2_Frame_Shift_Del_p.SR402fs|HAUS8_ENST00000253669.5_Frame_Shift_Del_p.SR403fs	p.SR342fs			Q9BT25	HAUS8_HUMAN			10	3044_3045	-			403					B4DJA7|C9JBZ4|Q49AC4|Q86WF0|Q96FX3	Frame_Shift_Del	DEL	ENST00000253669.5	37	c.1026_1027delTC	CCDS32948.1																																																																																				0.495	HAUS8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463015.1	NM_001011699		8	1122						8	1122	---	---	---	---
SLC7A9	11136	broad.mit.edu	37	19	33353391	33353393	+	In_Frame_Del	DEL	TGA	TGA	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr19:33353391_33353393delTGA	ENST00000023064.4	-	5	769_771	c.578_580delTCA	c.(577-582)atcagc>agc	p.I193del	SLC7A9_ENST00000587772.1_In_Frame_Del_p.I193del|RN7SKP22_ENST00000365097.1_RNA|SLC7A9_ENST00000590341.1_In_Frame_Del_p.I193del	NM_001126335.1|NM_001243036.1|NM_014270.4	NP_001119807.1|NP_001229965.1|NP_055085.1	P82251	BAT1_HUMAN	solute carrier family 7 (amino acid transporter light chain, bo,+ system), member 9	193			I -> II (in CSNU). {ECO:0000269|PubMed:11157794}.		amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|L-cystine transport (GO:0015811)|leukocyte migration (GO:0050900)|neutral amino acid transport (GO:0015804)|protein complex assembly (GO:0006461)|transmembrane transport (GO:0055085)|transport (GO:0006810)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|L-cystine transmembrane transporter activity (GO:0015184)|neutral amino acid transmembrane transporter activity (GO:0015175)|peptide antigen binding (GO:0042605)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	32	Esophageal squamous(110;0.137)				L-Cystine(DB00138)	ACCAGCCCGCTGATGATGATGAT	0.631																																					GBM(181;1335 2108 9644 44178 46689)	ENST00000023064.4																			0				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	32						c.(577-582)agc>a		solute carrier family 7 (amino acid transporter light chain, bo,+ system), member 9	L-Cystine(DB00138)																																			SO:0001651	inframe_deletion	11136				blood coagulation|cellular amino acid metabolic process|ion transport|leukocyte migration|protein complex assembly	integral to plasma membrane	L-cystine transmembrane transporter activity|neutral amino acid transmembrane transporter activity|peptide antigen binding	g.chr19:33353391_33353393delTGA	AF141289	CCDS12425.1	19q13.11	2013-07-19	2013-07-19		ENSG00000021488	ENSG00000021488		"""Solute carriers"""	11067	protein-coding gene	gene with protein product		604144		CSNU3		10471498	Standard	NM_014270		Approved		uc021usa.1	P82251	OTTHUMG00000180287	ENST00000023064.4:c.578_580delTCA	19.37:g.33353400_33353402delTGA	ENSP00000023064:p.Ile193del					SLC7A9_ENST00000590341.1_In_Frame_Del_p.IS193del|SLC7A9_ENST00000587772.1_In_Frame_Del_p.IS193del	p.IS193del	NM_001126335.1|NM_001243036.1|NM_014270.4	NP_001119807.1|NP_001229965.1|NP_055085.1	P82251	BAT1_HUMAN			5	769_771	-	Esophageal squamous(110;0.137)		193		I -> II (in CSNU).			B2R9A6	In_Frame_Del	DEL	ENST00000023064.4	37	c.578_580delTCA	CCDS12425.1																																																																																				0.631	SLC7A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450585.1			11	459						11	459	---	---	---	---
HAMP	57817	broad.mit.edu	37	19	35773520	35773522	+	In_Frame_Del	DEL	CTC	CTC	-	rs373178250		TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr19:35773520_35773522delCTC	ENST00000598398.1	+	2	336_338	c.40_42delCTC	c.(40-42)ctcdel	p.L18del	HAMP_ENST00000222304.3_In_Frame_Del_p.L18del	NM_021175.2	NP_066998.1	P81172	HEPC_HUMAN	hepcidin antimicrobial peptide	18					cellular iron ion homeostasis (GO:0006879)|defense response to bacterium (GO:0042742)|defense response to fungus (GO:0050832)|immune response (GO:0006955)|killing of cells of other organism (GO:0031640)	apical cortex (GO:0045179)|extracellular region (GO:0005576)				breast(1)|central_nervous_system(1)|large_intestine(1)|lung(1)	4	all_lung(56;2.37e-08)|Lung NSC(56;3.66e-08)|Esophageal squamous(110;0.162)		Epithelial(14;7.4e-20)|OV - Ovarian serous cystadenocarcinoma(14;6.47e-19)|all cancers(14;4.17e-17)|LUSC - Lung squamous cell carcinoma(66;0.0417)			TTGCCTCCTGCTCCTCCTCCTCC	0.64																																						ENST00000598398.1																			0				breast(1)|central_nervous_system(1)|large_intestine(1)|lung(1)	4						c.(40-42)del		hepcidin antimicrobial peptide																																				SO:0001651	inframe_deletion	57817				defense response to bacterium|defense response to fungus|immune response|killing of cells of other organism	extracellular region	hormone activity	g.chr19:35773520_35773522delCTC	AF309489	CCDS12454.1	19q13.1	2014-09-17				ENSG00000105697			15598	protein-coding gene	gene with protein product		606464				11034317, 11113132	Standard	NM_021175		Approved	LEAP-1, HEPC, HFE2B, LEAP1	uc002nyw.3	P81172		ENST00000598398.1:c.40_42delCTC	19.37:g.35773529_35773531delCTC	ENSP00000471894:p.Leu18del					HAMP_ENST00000222304.3_In_Frame_Del_p.L18del	p.L18del	NM_021175.2	NP_066998.1	P81172	HEPC_HUMAN	Epithelial(14;7.4e-20)|OV - Ovarian serous cystadenocarcinoma(14;6.47e-19)|all cancers(14;4.17e-17)|LUSC - Lung squamous cell carcinoma(66;0.0417)		2	336_338	+	all_lung(56;2.37e-08)|Lung NSC(56;3.66e-08)|Esophageal squamous(110;0.162)		18					Q1HE14|Q9BY68	In_Frame_Del	DEL	ENST00000598398.1	37	c.40_42delCTC	CCDS12454.1																																																																																				0.640	HAMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466067.1	NM_021175		14	1065						14	1065	---	---	---	---
ZNF585B	92285	broad.mit.edu	37	19	37681157	37681158	+	Intron	INS	-	-	T			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr19:37681157_37681158insT	ENST00000532828.2	-	3	324				CTC-454I21.3_ENST00000585860.2_Intron|ZNF585B_ENST00000586320.1_Intron|ZNF585B_ENST00000531805.1_De_novo_Start_OutOfFrame|ZNF585B_ENST00000527838.1_Intron	NM_152279.3	NP_689492.3	Q52M93	Z585B_HUMAN	zinc finger protein 585B						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(3)|endometrium(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)	29			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			AATTTACTTCAttttttttttg	0.46																																					Melanoma(93;882 1454 18863 28917 48427)	ENST00000531805.1																			0				NS(1)|breast(3)|endometrium(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)	29								zinc finger protein 585B																																				SO:0001627	intron_variant	92285				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|zinc ion binding	g.chr19:37681157_37681158insT	AK027834	CCDS12500.1	19q13.13	2013-01-08				ENSG00000245680		"""Zinc fingers, C2H2-type"", ""-"""	30948	protein-coding gene	gene with protein product						12477932	Standard	NM_152279		Approved	FLJ14928, SZFP41	uc002ofq.3	Q52M93		ENST00000532828.2:c.73-105->A	19.37:g.37681167_37681167dupT						ZNF585B_ENST00000527838.1_Intron|CTC-454I21.3_ENST00000585860.2_Intron|ZNF585B_ENST00000586320.1_Intron|ZNF585B_ENST00000532828.2_Intron				Q52M93	Z585B_HUMAN	COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)		0	220_221	-								Q8IZD3|Q96JW6	Translation_Start_Site	INS	ENST00000532828.2	37		CCDS12500.1																																																																																				0.460	ZNF585B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388272.2	NM_152279		9	119						9	119	---	---	---	---
SPRED3	399473	broad.mit.edu	37	19	38882864	38882866	+	In_Frame_Del	DEL	CCT	CCT	-	rs151129136		TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr19:38882864_38882866delCCT	ENST00000338502.4	+	3	462_464	c.359_361delCCT	c.(358-363)ccctcc>ccc	p.S128del	SPRED3_ENST00000587013.1_In_Frame_Del_p.S172del|SPRED3_ENST00000587564.2_3'UTR|SPRED3_ENST00000586301.1_In_Frame_Del_p.S128del	NM_001042522.2	NP_001035987.1	Q2MJR0	SPRE3_HUMAN	sprouty-related, EVH1 domain containing 3	128	Ser-rich.				inactivation of MAPK activity (GO:0000188)|multicellular organismal development (GO:0007275)	plasma membrane (GO:0005886)				central_nervous_system(2)|large_intestine(1)|lung(5)|skin(1)	9	all_cancers(60;3.4e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			TCACTCAccccctcctcctcctc	0.645																																						ENST00000587013.1																			0				central_nervous_system(2)|large_intestine(1)|lung(5)|skin(1)	9						c.(490-495)ccc>c		sprouty-related, EVH1 domain containing 3			,	401,4,3395		26,0,349,0,4,1521					,	3.3	0.9		dbSNP_134	44	1035,11,6892		107,0,821,1,9,3031	no	codingComplex,codingComplex	SPRED3	NM_001042522.1,NM_001039616.1	,	133,0,1170,1,13,4552	A1A1,A1A2,A1R,A2A2,A2R,RR		13.1771,10.6579,12.3616	,	,		1436,15,10287				SO:0001651	inframe_deletion	399473				multicellular organismal development			g.chr19:38882864_38882866delCCT		CCDS42560.1	19q13	2007-10-05				ENSG00000188766			31041	protein-coding gene	gene with protein product		609293				14618415	Standard	NM_001042522		Approved		uc002oim.4	Q2MJR0		ENST00000338502.4:c.359_361delCCT	19.37:g.38882873_38882875delCCT	ENSP00000345405:p.Ser128del					SPRED3_ENST00000586301.1_In_Frame_Del_p.PS120del|SPRED3_ENST00000587564.2_3'UTR|SPRED3_ENST00000338502.4_In_Frame_Del_p.PS120del	p.PS164del			Q2MJR0	SPRE3_HUMAN	Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		3	569_571	+	all_cancers(60;3.4e-06)		120					Q2MJR1	In_Frame_Del	DEL	ENST00000338502.4	37	c.491_493delCCT	CCDS42560.1																																																																																				0.645	SPRED3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459216.1	XM_351191		10	147						10	147	---	---	---	---
RYR1	6261	broad.mit.edu	37	19	38948159	38948160	+	Frame_Shift_Del	DEL	TG	TG	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr19:38948159_38948160delTG	ENST00000359596.3	+	17	1814_1815	c.1814_1815delTG	c.(1813-1815)ctgfs	p.L605fs	RYR1_ENST00000360985.3_Frame_Shift_Del_p.L605fs|RYR1_ENST00000355481.4_Frame_Shift_Del_p.L605fs			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	605	B30.2/SPRY 1. {ECO:0000255|PROSITE- ProRule:PRU00548}.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	CTATGCTCCCTGTGTGTGTGTA	0.53																																						ENST00000355481.4																			0				NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285						c.(1813-1815)cfs		ryanodine receptor 1 (skeletal)	Dantrolene(DB01219)																																			SO:0001589	frameshift_variant	6261				muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia	cell cortex|cytosol|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna	calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity	g.chr19:38948159_38948160delTG	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.1814_1815delTG	19.37:g.38948167_38948168delTG	ENSP00000352608:p.Leu605fs					RYR1_ENST00000360985.3_Frame_Shift_Del_p.L605fs|RYR1_ENST00000359596.3_Frame_Shift_Del_p.L605fs	p.L605fs	NM_000540.2|NM_001042723.1	NP_000531.2|NP_001036188.1	P21817	RYR1_HUMAN	Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		17	1945_1946	+	all_cancers(60;7.91e-06)		605			B30.2/SPRY 1.		Q16314|Q16368|Q9NPK1|Q9P1U4	Frame_Shift_Del	DEL	ENST00000359596.3	37	c.1814_1815delTG	CCDS33011.1																																																																																				0.530	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			9	1195						9	1195	---	---	---	---
TIMM50	92609	broad.mit.edu	37	19	39972604	39972604	+	Frame_Shift_Del	DEL	A	A	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr19:39972604delA	ENST00000607714.1	+	2	212	c.190delA	c.(190-192)aaafs	p.K65fs	TIMM50_ENST00000599794.1_Intron|TIMM50_ENST00000544017.1_5'UTR|TIMM50_ENST00000314349.4_Frame_Shift_Del_p.K168fs			Q3ZCQ8	TIM50_HUMAN	translocase of inner mitochondrial membrane 50 homolog (S. cerevisiae)	65					cellular protein metabolic process (GO:0044267)|mitochondrial membrane organization (GO:0007006)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein targeting to mitochondrion (GO:0006626)|release of cytochrome c from mitochondria (GO:0001836)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial inner membrane presequence translocase complex (GO:0005744)|mitochondrion (GO:0005739)|nuclear speck (GO:0016607)	interleukin-2 receptor binding (GO:0005134)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|ribonucleoprotein complex binding (GO:0043021)|RNA binding (GO:0003723)			NS(1)|endometrium(3)|large_intestine(5)|lung(3)|ovary(1)|prostate(1)	14	all_cancers(60;4.04e-06)|all_lung(34;1.77e-07)|Lung NSC(34;2.09e-07)|all_epithelial(25;1.13e-05)|Ovarian(47;0.159)		Epithelial(26;5.89e-26)|all cancers(26;1.96e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			CAGCTATGCCAAAAAAGTTGC	0.607																																						ENST00000314349.4																			0				NS(1)|endometrium(3)|large_intestine(5)|lung(3)|ovary(1)|prostate(1)	14						c.(499-501)aafs		translocase of inner mitochondrial membrane 50 homolog (S. cerevisiae)							114.0	123.0	120.0					19																	39972604		2203	4300	6503	SO:0001589	frameshift_variant	92609				mitochondrial membrane organization|protein transport|release of cytochrome c from mitochondria|transmembrane transport	integral to membrane|mitochondrial inner membrane presequence translocase complex|nuclear speck	interleukin-2 receptor binding|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|ribonucleoprotein binding|RNA binding	g.chr19:39972604delA	BC009072	CCDS33023.1	19q13.2	2010-06-21	2006-04-04		ENSG00000105197	ENSG00000105197		"""Serine/threonine phosphatases / CTD aspartate-based phosphatases"""	23656	protein-coding gene	gene with protein product		607381	"""translocase of inner mitochondrial membrane 50 homolog (yeast)"""			12437925	Standard	NM_001001563		Approved	TIM50L	uc002olu.1	Q3ZCQ8		ENST00000607714.1:c.190delA	19.37:g.39972604delA	ENSP00000475531:p.Lys65fs					TIMM50_ENST00000599794.1_Intron|TIMM50_ENST00000544017.1_5'UTR|TIMM50_ENST00000607714.1_Frame_Shift_Del_p.K65fs	p.K168fs	NM_001001563.1	NP_001001563.1	Q3ZCQ8	TIM50_HUMAN	Epithelial(26;5.89e-26)|all cancers(26;1.96e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)		2	632	+	all_cancers(60;4.04e-06)|all_lung(34;1.77e-07)|Lung NSC(34;2.09e-07)|all_epithelial(25;1.13e-05)|Ovarian(47;0.159)		65			FCP1 homology.		Q330K1|Q6QA00|Q96FJ5|Q96GY2|Q9H370	Frame_Shift_Del	DEL	ENST00000607714.1	37	c.499delA																																																																																					0.607	TIMM50-021	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470728.1	NM_001001563		7	913						7	913	---	---	---	---
PSG7	5676	broad.mit.edu	37	19	43440068	43440069	+	RNA	DEL	AC	AC	-	rs147024666		TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr19:43440068_43440069delAC	ENST00000406070.2	-	0	161				PSG7_ENST00000446844.3_RNA|PSG7_ENST00000471557.1_RNA	NM_002783.2	NP_002774.2	Q13046	PSG7_HUMAN	pregnancy specific beta-1-glycoprotein 7 (gene/pseudogene)						female pregnancy (GO:0007565)	extracellular region (GO:0005576)							Prostate(69;0.00682)				acacacacaaacacacacacac	0.495																																						ENST00000406070.2																			0													pregnancy specific beta-1-glycoprotein 7 (gene/pseudogene)																																						5676				female pregnancy	extracellular region		g.chr19:43440068_43440069delAC			19q13.2	2013-01-29	2010-02-26		ENSG00000221878	ENSG00000221878		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9524	protein-coding gene	gene with protein product		176396	"""pregnancy specific beta-1-glycoprotein 7"""				Standard	NM_002783		Approved		uc010xwl.2	Q13046	OTTHUMG00000151125		19.37:g.43440078_43440079delAC						PSG7_ENST00000446844.3_RNA		NM_002783.2	NP_002774.2	Q13046	PSG7_HUMAN			0	161	-		Prostate(69;0.00682)						Q15232	RNA	DEL	ENST00000406070.2	37																																																																																						0.495	PSG7-001	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000321431.2	NM_001206650		7	144						7	144	---	---	---	---
CD3EAP	10849	broad.mit.edu	37	19	45911859	45911861	+	In_Frame_Del	DEL	GAA	GAA	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr19:45911859_45911861delGAA	ENST00000309424.3	+	3	1121_1123	c.633_635delGAA	c.(631-636)cggaag>cgg	p.K217del	ERCC1_ENST00000300853.3_3'UTR|ERCC1_ENST00000588738.1_5'Flank|CD3EAP_ENST00000589804.1_In_Frame_Del_p.K219del|ERCC1_ENST00000423698.2_3'UTR|PPP1R13L_ENST00000418234.2_5'Flank	NM_012099.1	NP_036231.1	O15446	RPA34_HUMAN	CD3e molecule, epsilon associated protein	217	Poly-Lys.				rRNA transcription (GO:0009303)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|DNA-directed RNA polymerase I complex (GO:0005736)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|RNA polymerase I transcription factor complex (GO:0000120)	DNA-directed RNA polymerase activity (GO:0003899)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)	11		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0251)		TGGATGTGCGGAAGAAGAAGAAG	0.581																																						ENST00000309424.3																			0				breast(2)|endometrium(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)	11						c.(631-636)cgg>cg		CD3e molecule, epsilon associated protein			,,	0,144,4118		0,0,0,13,118,2000					,,	-5.6	0.0			66	5,183,8058		0,0,5,3,177,3938	no	codingComplex,utr-3,utr-3	ERCC1,CD3EAP	NM_012099.1,NM_001983.3,NM_001166049.1	,,	0,0,5,16,295,5938	A1A1,A1A2,A1R,A2A2,A2R,RR		2.2799,3.3787,2.6543	,,	,,		5,327,12176				SO:0001651	inframe_deletion	10849				rRNA transcription|transmembrane receptor protein tyrosine kinase signaling pathway	chromosome|RNA polymerase I transcription factor complex	DNA-directed RNA polymerase activity	g.chr19:45911859_45911861delGAA	U86751	CCDS12661.1, CCDS74397.1	19q13.3	2008-02-05	2006-03-28			ENSG00000117877			24219	protein-coding gene	gene with protein product	"""CD3 epsilon associated protein"", ""antisense to ERCC 1"""	107325	"""CD3e antigen, epsilon polypeptide associated protein"""			10373416, 9426281, 15226435	Standard	XM_005258425		Approved	ASE-1, CAST, PAF49	uc002pbq.1	O15446		ENST00000309424.3:c.633_635delGAA	19.37:g.45911868_45911870delGAA	ENSP00000310966:p.Lys217del					CD3EAP_ENST00000589804.1_In_Frame_Del_p.RK213del|ERCC1_ENST00000300853.3_3'UTR|ERCC1_ENST00000423698.2_3'UTR	p.RK211del	NM_012099.1	NP_036231.1	O15446	RPA34_HUMAN		OV - Ovarian serous cystadenocarcinoma(262;0.0251)	3	1121_1123	+		all_neural(266;0.224)|Ovarian(192;0.231)	211					Q32N11|Q7Z5U2|Q9UPF6	In_Frame_Del	DEL	ENST00000309424.3	37	c.633_635delGAA	CCDS12661.1																																																																																				0.581	CD3EAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459538.1	NM_012099		18	776						18	776	---	---	---	---
LILRB1	10859	broad.mit.edu	37	19	55146148	55146150	+	In_Frame_Del	DEL	CTC	CTC	-	rs543059448	byFrequency	TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr19:55146148_55146150delCTC	ENST00000396331.1	+	11	1774_1776	c.1417_1419delCTC	c.(1417-1419)ctcdel	p.L479del	LILRB1_ENST00000434867.2_In_Frame_Del_p.L479del|LILRB1_ENST00000396327.3_In_Frame_Del_p.L480del|LILRB1_ENST00000324602.7_In_Frame_Del_p.L480del|LILRB1_ENST00000396317.1_In_Frame_Del_p.L463del|LILRB1_ENST00000448689.1_In_Frame_Del_p.L479del|LILRB1_ENST00000396315.1_In_Frame_Del_p.L480del|LILRB1_ENST00000418536.2_In_Frame_Del_p.L463del|LILRB1_ENST00000462628.1_3'UTR|LILRB1_ENST00000396332.4_In_Frame_Del_p.L479del|LILRB1_ENST00000427581.2_In_Frame_Del_p.L529del|LILRB1_ENST00000396321.2_In_Frame_Del_p.L479del	NM_006669.3	NP_006660.3	Q8NHL6	LIRB1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1	479					cellular response to lipopolysaccharide (GO:0071222)|defense response to virus (GO:0051607)|dendritic cell differentiation (GO:0097028)|Fc receptor mediated inhibitory signaling pathway (GO:0002774)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma production (GO:0032609)|interferon-gamma secretion (GO:0072643)|negative regulation of alpha-beta T cell activation (GO:0046636)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of CD8-positive, alpha-beta T cell activation (GO:2001186)|negative regulation of cell cycle (GO:0045786)|negative regulation of cytokine secretion involved in immune response (GO:0002740)|negative regulation of dendritic cell apoptotic process (GO:2000669)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of endocytosis (GO:0045806)|negative regulation of interferon-beta secretion (GO:0035548)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-10 secretion (GO:2001180)|negative regulation of interleukin-12 secretion (GO:2001183)|negative regulation of mononuclear cell proliferation (GO:0032945)|negative regulation of natural killer cell mediated cytotoxicity (GO:0045953)|negative regulation of osteoclast development (GO:2001205)|negative regulation of serotonin secretion (GO:0014063)|negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:2001189)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transforming growth factor-beta secretion (GO:2001202)|negative regulation of tumor necrosis factor biosynthetic process (GO:0042536)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytolysis (GO:0045919)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of gamma-delta T cell activation involved in immune response (GO:2001193)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor internalization (GO:0031623)|regulation of immune response (GO:0050776)|response to virus (GO:0009615)|signal transduction (GO:0007165)|T cell proliferation involved in immune response (GO:0002309)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	HLA-A specific inhibitory MHC class I receptor activity (GO:0030107)|HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)|MHC class I protein binding (GO:0042288)|MHC class I receptor activity (GO:0032393)|protein homodimerization activity (GO:0042803)|protein phosphatase 1 binding (GO:0008157)|SH2 domain binding (GO:0042169)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(38)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	74				GBM - Glioblastoma multiforme(193;0.0188)		CAtcctactgctcctcctcctcc	0.581										HNSCC(37;0.09)				8	0.00159744	0.0023	0.0014	5008	,	,		18237	0.002		0.001	False		,,,				2504	0.001					ENST00000396331.1																			0				NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(38)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	74						c.(1417-1419)del		leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1			,,,	21,4241		0,21,2110					,,,	0.7	0.0			137	49,8205		0,49,4078	no	coding,coding,coding,coding	LILRB1	NM_006669.3,NM_001081639.1,NM_001081638.1,NM_001081637.1	,,,	0,70,6188	A1A1,A1R,RR		0.5937,0.4927,0.5593	,,,	,,,		70,12446				SO:0001651	inframe_deletion	0				regulation of immune response|response to virus	integral to membrane|plasma membrane	protein phosphatase 1 binding|receptor activity	g.chr19:55146148_55146150delCTC	AF009220	CCDS42614.1, CCDS42615.1, CCDS42616.1, CCDS42617.1, CCDS62803.1	19q13.4	2013-01-11						"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6605	protein-coding gene	gene with protein product		604811				9285411, 9382880	Standard	XM_006726246		Approved	LIR-1, ILT2, MIR-7, CD85, LIR1, CD85j	uc002qgm.3	Q8NHL6		ENST00000396331.1:c.1417_1419delCTC	19.37:g.55146157_55146159delCTC	ENSP00000379622:p.Leu479del	HNSCC(37;0.09)				LILRB1_ENST00000396332.4_In_Frame_Del_p.L479del|LILRB1_ENST00000418536.2_In_Frame_Del_p.L463del|LILRB1_ENST00000427581.2_In_Frame_Del_p.L529del|LILRB1_ENST00000462628.1_3'UTR|LILRB1_ENST00000396315.1_In_Frame_Del_p.L480del|LILRB1_ENST00000448689.1_In_Frame_Del_p.L479del|LILRB1_ENST00000324602.7_In_Frame_Del_p.L480del|LILRB1_ENST00000434867.2_In_Frame_Del_p.L479del|LILRB1_ENST00000396317.1_In_Frame_Del_p.L463del|LILRB1_ENST00000396321.2_In_Frame_Del_p.L479del|LILRB1_ENST00000396327.3_In_Frame_Del_p.L480del	p.L479del	NM_006669.3	NP_006660.3	Q8NHL6	LIRB1_HUMAN		GBM - Glioblastoma multiforme(193;0.0188)	11	1774_1776	+			479					A2IXV4|A8MXT0|O75024|O75025|Q8NHJ9|Q8NHK0	In_Frame_Del	DEL	ENST00000396331.1	37	c.1417_1419delCTC	CCDS42617.1																																																																																				0.581	LILRB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140796.4			8	387						8	387	---	---	---	---
PTTG1IP	754	broad.mit.edu	37	21	46276194	46276196	+	In_Frame_Del	DEL	GCA	GCA	-	rs375347383		TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr21:46276194_46276196delGCA	ENST00000330938.3	-	4	581_583	c.361_363delTGC	c.(361-363)tgcdel	p.C121del	PTTG1IP_ENST00000397887.3_Intron|PTTG1IP_ENST00000445724.2_Intron|PTTG1IP_ENST00000494690.1_5'UTR|PTTG1IP_ENST00000397886.3_In_Frame_Del_p.C100del	NM_004339.3	NP_004330.1	P53801	PTTG_HUMAN	pituitary tumor-transforming 1 interacting protein	121	Poly-Cys.				multicellular organismal development (GO:0007275)|protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	receptor activity (GO:0004872)			ovary(1)|prostate(1)	2				Colorectal(79;0.0659)		TCTTCCTCCTGCAGCAGCAGCAG	0.616																																						ENST00000330938.3																			0				ovary(1)|prostate(1)	2						c.(361-363)del		pituitary tumor-transforming 1 interacting protein																																				SO:0001651	inframe_deletion	754				protein import into nucleus	cytoplasm|integral to membrane|nucleus		g.chr21:46276194_46276196delGCA	AF149785	CCDS13715.1, CCDS68221.1	21q22.3	2008-07-04			ENSG00000183255	ENSG00000183255			13524	protein-coding gene	gene with protein product		603784		C21orf3, C21orf1		9570958, 10830953	Standard	NM_004339		Approved	PBF	uc002zgb.2	P53801	OTTHUMG00000090254	ENST00000330938.3:c.361_363delTGC	21.37:g.46276203_46276205delGCA	ENSP00000328325:p.Cys121del					PTTG1IP_ENST00000397887.3_Intron|PTTG1IP_ENST00000397886.3_In_Frame_Del_p.C100del|PTTG1IP_ENST00000494690.1_5'UTR|PTTG1IP_ENST00000445724.2_Intron	p.C121del	NM_004339.3	NP_004330.1	P53801	PTTG_HUMAN		Colorectal(79;0.0659)	4	581_583	-			121			Poly-Cys.		B2RDP7|D3DSL9|Q9NS09	In_Frame_Del	DEL	ENST00000330938.3	37	c.361_363delTGC	CCDS13715.1																																																																																				0.616	PTTG1IP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206553.1			9	381						9	381	---	---	---	---
PICK1	9463	broad.mit.edu	37	22	38471034	38471036	+	In_Frame_Del	DEL	GGA	GGA	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr22:38471034_38471036delGGA	ENST00000404072.3	+	13	1490_1492	c.1143_1145delGGA	c.(1141-1146)ggggag>ggg	p.E388del	PICK1_ENST00000356976.3_In_Frame_Del_p.E388del|RP5-1039K5.13_ENST00000445483.1_RNA	NM_001039583.1|NM_001039584.1	NP_001034672.1|NP_001034673.1	Q9NRD5	PICK1_HUMAN	protein interacting with PRKCA 1	388	Poly-Glu.				ATP catabolic process (GO:0006200)|cellular response to decreased oxygen levels (GO:0036294)|cellular response to glucose starvation (GO:0042149)|dendritic spine maintenance (GO:0097062)|dendritic spine organization (GO:0097061)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|glial cell development (GO:0021782)|long term synaptic depression (GO:0060292)|monoamine transport (GO:0015844)|negative regulation of Arp2/3 complex-mediated actin nucleation (GO:0034316)|neuronal ion channel clustering (GO:0045161)|positive regulation of receptor internalization (GO:0002092)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein phosphorylation (GO:0006468)|protein targeting (GO:0006605)|receptor clustering (GO:0043113)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|endocytic vesicle membrane (GO:0030666)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synapse (GO:0045202)	actin filament binding (GO:0051015)|Arp2/3 complex binding (GO:0071933)|ATPase activity (GO:0016887)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein kinase C binding (GO:0005080)|receptor binding (GO:0005102)			cervix(1)|endometrium(3)|large_intestine(1)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	13	Melanoma(58;0.045)					TCACAGATGGggaggaggaggag	0.635																																						ENST00000404072.3																			0				cervix(1)|endometrium(3)|large_intestine(1)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	13						c.(1141-1146)ggg>gg		protein interacting with PRKCA 1																																				SO:0001651	inframe_deletion	9463				activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|DNA methylation involved in embryo development|DNA methylation involved in gamete generation|monoamine transport|neuronal ion channel clustering|protein phosphorylation|receptor clustering|retrograde vesicle-mediated transport, Golgi to ER|synaptic transmission	cell junction|endocytic vesicle membrane|Golgi apparatus|perinuclear region of cytoplasm|presynaptic membrane	ATPase activity|metal ion binding|protein C-terminus binding|protein kinase C binding|receptor binding	g.chr22:38471034_38471036delGGA	AL049654	CCDS13965.1	22q13.1	2006-02-14	2006-02-14	2006-02-14	ENSG00000100151	ENSG00000100151			9394	protein-coding gene	gene with protein product		605926	"""protein kinase C, alpha binding protein"", ""protein interacting with PRKCA"""	PRKCABP		10340301, 10591208	Standard	XM_006724377		Approved	dJ1039K5, MGC15204	uc003aus.3	Q9NRD5	OTTHUMG00000151159	ENST00000404072.3:c.1143_1145delGGA	22.37:g.38471043_38471045delGGA	ENSP00000385205:p.Glu388del					PICK1_ENST00000356976.3_In_Frame_Del_p.GE381del	p.GE381del	NM_001039583.1|NM_001039584.1	NP_001034672.1|NP_001034673.1	Q9NRD5	PICK1_HUMAN			13	1490_1492	+	Melanoma(58;0.045)		381					B3KS52|O95906	In_Frame_Del	DEL	ENST00000404072.3	37	c.1143_1145delGGA	CCDS13965.1																																																																																				0.635	PICK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321569.2	NM_012407		7	163						7	163	---	---	---	---
SERHL	94009	broad.mit.edu	37	22	42898666	42898666	+	RNA	DEL	C	C	-	rs375411583	byFrequency	TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chr22:42898666delC	ENST00000359906.2	+	0	409					NR_027786.1		Q9NQF3	SERHL_HUMAN	serine hydrolase-like								hydrolase activity (GO:0016787)			endometrium(1)|large_intestine(1)	2						CCATATGGTGCCCCCCCCCCA	0.592													|||unknown(HR)	137	0.0273562	0.0348	0.0288	5008	,	,		27362	0.0268		0.0129	False		,,,				2504	0.0317					ENST00000359906.2																			0				endometrium(1)|large_intestine(1)	2								serine hydrolase-like				58,659,3511		2,0,54,4,651,1403						0.9	0.1			70	152,913,7063		5,1,141,0,912,3005	no	intergenic				7,1,195,4,1563,4408	A1A1,A1A2,A1R,A2A2,A2R,RR		13.1029,16.9584,14.4221				210,1572,10574						94009							g.chr22:42898666delC	AL365513		22q13.2-q13.31	2009-10-06				ENSG00000172250			14408	protein-coding gene	gene with protein product	"""kraken-like"""	607979				11352564	Standard	NR_027786		Approved	HS126B42, BK126B4.1, dJ222E13.1	uc021wql.1	Q9NQF3			22.37:g.42898666delC								NR_027786.1						0	409	+								Q5JZ95|Q9UH21	RNA	DEL	ENST00000359906.2	37																																																																																						0.592	SERHL-001	KNOWN	basic	antisense	processed_transcript	OTTHUMT00000320498.2	NM_170694		11	153						11	153	---	---	---	---
OFD1	8481	broad.mit.edu	37	X	13764946	13764946	+	Frame_Shift_Del	DEL	A	A	-	rs312262846|rs312262847|rs312262848		TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chrX:13764946delA	ENST00000340096.6	+	8	1029	c.702delA	c.(700-702)gcafs	p.A234fs	OFD1_ENST00000380550.3_Frame_Shift_Del_p.A234fs|OFD1_ENST00000490265.1_3'UTR|OFD1_ENST00000380567.1_Frame_Shift_Del_p.A94fs|OFD1_ENST00000398395.3_Frame_Shift_Del_p.A234fs	NM_003611.2	NP_003602.1	O75665	OFD1_HUMAN	oral-facial-digital syndrome 1	234					axoneme assembly (GO:0035082)|cilium morphogenesis (GO:0060271)|embryonic body morphogenesis (GO:0010172)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of fibroblast growth factor receptor signaling pathway involved in neural plate anterior/posterior pattern formation (GO:2000314)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytosol (GO:0005829)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	alpha-tubulin binding (GO:0043014)|gamma-tubulin binding (GO:0043015)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	25						AAATGGAAGCAAAAAAAAAGT	0.299																																						ENST00000380567.1																			0				breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	25						c.(280-282)gcfs		oral-facial-digital syndrome 1				31,3690		0,25,6,1567,531	48.0	47.0	47.0			4.2	1.0	X		47	88,6391		4,29,51,2322,1718	no	frameshift	OFD1	NM_003611.2		4,54,57,3889,2249	A1A1,A1R,A1,RR,R		1.3582,0.8331,1.1667			13764946	119,10081	2203	4298	6501	SO:0001589	frameshift_variant	8481				cilium movement involved in determination of left/right asymmetry|G2/M transition of mitotic cell cycle	centriole|cilium|cytosol|microtubule basal body|nuclear membrane	alpha-tubulin binding|gamma-tubulin binding	g.chrX:13764946delA	Y15164	CCDS14157.1	Xp22	2014-06-18			ENSG00000046651	ENSG00000046651			2567	protein-coding gene	gene with protein product		300170	"""retinitis pigmentosa 23 (X-linked recessive)"""	CXorf5, RP23		9722947, 9215688, 22619378	Standard	NM_003611		Approved	71-7A, JBTS10	uc004cvp.4	O75665	OTTHUMG00000021159	ENST00000340096.6:c.702delA	X.37:g.13764946delA	ENSP00000344314:p.Ala234fs					OFD1_ENST00000398395.3_Frame_Shift_Del_p.A234fs|OFD1_ENST00000340096.6_Frame_Shift_Del_p.A234fs|OFD1_ENST00000490265.1_3'UTR|OFD1_ENST00000380550.3_Frame_Shift_Del_p.A234fs	p.A94fs			O75665	OFD1_HUMAN			9	1154	+			234			LisH.		B9ZVU5|O75666|Q4VAK4	Frame_Shift_Del	DEL	ENST00000340096.6	37	c.282delA	CCDS14157.1																																																																																				0.299	OFD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055808.1	NM_003611		14	364						14	364	---	---	---	---
PRRG1	5638	broad.mit.edu	37	X	37312611	37312611	+	Frame_Shift_Del	DEL	C	C	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chrX:37312611delC	ENST00000542554.1	+	5	666	c.394delC	c.(394-396)cccfs	p.P135fs	PRRG1_ENST00000491253.1_3'UTR|PRRG1_ENST00000378628.4_Frame_Shift_Del_p.P135fs|PRRG1_ENST00000543642.1_Frame_Shift_Del_p.P135fs|PRRG1_ENST00000449135.2_Frame_Shift_Del_p.P135fs|TM4SF2_ENST00000465127.1_Intron	NM_001173489.1	NP_001166960.1	O14668	TMG1_HUMAN	proline rich Gla (G-carboxyglutamic acid) 1	135	Poly-Pro.					extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.P135fs*3(1)|p.P134fs*19(1)		breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	15						TATCACCCCACCCCCCCCACC	0.488																																						ENST00000542554.1																			2	Deletion - Frameshift(1)|Insertion - Frameshift(1)	p.P135fs*3(1)|p.P134fs*19(1)	ovary(2)	breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	15						c.(394-396)ccfs		proline rich Gla (G-carboxyglutamic acid) 1							117.0	111.0	113.0					X																	37312611		2202	4300	6502	SO:0001589	frameshift_variant	5638					extracellular region|integral to plasma membrane	calcium ion binding	g.chrX:37312611delC	AF009242	CCDS14239.1, CCDS55397.1	Xp21.1	2010-08-13	2004-05-27		ENSG00000130962	ENSG00000130962			9469	protein-coding gene	gene with protein product		604428	"""proline-rich Gla (G-carboxyglutamic acid) polypeptide 1"""			9256434	Standard	NM_000950		Approved	PRGP1	uc004ddo.3	O14668	OTTHUMG00000021360	ENST00000542554.1:c.394delC	X.37:g.37312611delC	ENSP00000444278:p.Pro135fs					PRRG1_ENST00000543642.1_Frame_Shift_Del_p.P135fs|PRRG1_ENST00000449135.2_Frame_Shift_Del_p.P135fs|PRRG1_ENST00000378628.4_Frame_Shift_Del_p.P135fs|TM4SF2_ENST00000465127.1_Intron|PRRG1_ENST00000491253.1_3'UTR	p.P135fs	NM_001173489.1	NP_001166960.1	O14668	TMG1_HUMAN			5	666	+			135			Poly-Pro.		B2R7A3|C9JXL7|D3DWA9|Q5JT66	Frame_Shift_Del	DEL	ENST00000542554.1	37	c.394delC	CCDS14239.1																																																																																				0.488	PRRG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056228.2	NM_000950		8	807						8	807	---	---	---	---
SRPX	8406	broad.mit.edu	37	X	38079976	38079978	+	In_Frame_Del	DEL	GCA	GCA	-	rs35523939|rs72249350|rs139109693		TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chrX:38079976_38079978delGCA	ENST00000378533.3	-	1	174_176	c.68_70delTGC	c.(67-72)ctgcgc>cgc	p.L23del	TM4SF2_ENST00000465127.1_Intron|SRPX_ENST00000544439.1_In_Frame_Del_p.L23del|SRPX_ENST00000343800.6_Intron|SRPX_ENST00000538295.1_In_Frame_Del_p.L23del|SRPX_ENST00000432886.2_In_Frame_Del_p.L23del|RP13-43E11.1_ENST00000423919.1_RNA	NM_006307.4	NP_006298.1	P78539	SRPX_HUMAN	sushi-repeat containing protein, X-linked	23			Missing. {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:8634709, ECO:0000269|PubMed:9162095}.		autophagy (GO:0006914)|cell adhesion (GO:0007155)|negative regulation of cell proliferation involved in contact inhibition (GO:0060244)|phagolysosome assembly (GO:0001845)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|response to endoplasmic reticulum stress (GO:0034976)	autophagic vacuole (GO:0005776)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)		p.L23delL(2)		autonomic_ganglia(1)|breast(2)|endometrium(5)|large_intestine(5)|lung(10)|prostate(2)	25						GGCGGGACGCgcagcagcagcag	0.729											OREG0019726	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		636	0.168477	0.1657	0.1398	3775	,	,		8591	0.0129		0.2028	False		,,,				2504	0.1053					ENST00000378533.3																			2	Deletion - In frame(2)	p.L23delL(2)	prostate(2)	autonomic_ganglia(1)|breast(2)|endometrium(5)|large_intestine(5)|lung(10)|prostate(2)	25						c.(67-72)cgc>c		sushi-repeat containing protein, X-linked																																				SO:0001651	inframe_deletion	8406				cell adhesion	cell surface|membrane		g.chrX:38079976_38079978delGCA	U78093	CCDS14245.1, CCDS55400.1, CCDS55401.1, CCDS55402.1	Xp21.1	2011-01-25	2011-01-25		ENSG00000101955	ENSG00000101955			11309	protein-coding gene	gene with protein product		300187	"""sushi-repeat-containing protein, X chromosome"", ""sushi-repeat-containing protein, X-linked"""			8634708, 8634709	Standard	NM_006307		Approved	ETX1	uc004ddy.2	P78539	OTTHUMG00000021362	ENST00000378533.3:c.68_70delTGC	X.37:g.38079985_38079987delGCA	ENSP00000367794:p.Leu23del		OREG0019726	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	875	SRPX_ENST00000432886.2_In_Frame_Del_p.LR23del|SRPX_ENST00000544439.1_In_Frame_Del_p.LR23del|TM4SF2_ENST00000465127.1_Intron|SRPX_ENST00000538295.1_In_Frame_Del_p.LR23del|SRPX_ENST00000343800.6_Intron	p.LR23del	NM_006307.4	NP_006298.1	P78539	SRPX_HUMAN			1	174_176	-			23		Missing.			A8K065|B3KWP8|B4DDB8|B4DQH5|F5H4D7|G3V1L0|Q4VX66|Q99652|Q99913	In_Frame_Del	DEL	ENST00000378533.3	37	c.68_70delTGC	CCDS14245.1																																																																																				0.729	SRPX-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056243.1	NM_006307		18	26						18	26	---	---	---	---
MED12	9968	broad.mit.edu	37	X	70360589	70360591	+	In_Frame_Del	DEL	AGC	AGC	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chrX:70360589_70360591delAGC	ENST00000374080.3	+	42	6181_6183	c.6149_6151delAGC	c.(6148-6153)gagcag>gag	p.Q2076del	MED12_ENST00000374102.1_In_Frame_Del_p.Q2075del|MED12_ENST00000333646.6_In_Frame_Del_p.Q2079del|AL590764.1_ENST00000579622.1_RNA			Q93074	MED12_HUMAN	mediator complex subunit 12	2076	Gln-rich.				androgen receptor signaling pathway (GO:0030521)|axis elongation involved in somitogenesis (GO:0090245)|canonical Wnt signaling pathway (GO:0060070)|gene expression (GO:0010467)|heart development (GO:0007507)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|oligodendrocyte development (GO:0014003)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|Schwann cell development (GO:0014044)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|receptor activity (GO:0004872)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II transcription cofactor activity (GO:0001104)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(6)|central_nervous_system(2)|endometrium(22)|kidney(5)|large_intestine(8)|lung(31)|ovary(2)|pancreas(1)|prostate(11)|skin(5)|soft_tissue(323)|upper_aerodigestive_tract(1)|urinary_tract(3)	420	Renal(35;0.156)					ATCCTACCTGagcagcagcagca	0.586			"""M, S"""		uterine leiomyoma		Opitz-Kaveggia Syndrome																															ENST00000333646.6				Dom	yes		X	Xq13	9968	"""M, S"""	mediator complex subunit 12	Yes	Opitz-Kaveggia Syndrome	M			uterine leiomyoma		0				breast(6)|central_nervous_system(2)|endometrium(22)|kidney(5)|large_intestine(8)|lung(31)|ovary(2)|pancreas(1)|prostate(11)|skin(5)|soft_tissue(323)|upper_aerodigestive_tract(1)|urinary_tract(3)	420						c.(6157-6162)gag>g		mediator complex subunit 12																																				SO:0001651	inframe_deletion	9968				androgen receptor signaling pathway|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|protein C-terminus binding|protein domain specific binding|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding	g.chrX:70360589_70360591delAGC	U80742	CCDS43970.1	Xq13	2011-02-14	2007-07-30	2004-11-26	ENSG00000184634	ENSG00000184634			11957	protein-coding gene	gene with protein product		300188	"""trinucleotide repeat containing 11 (THR-associated protein, 230kDa subunit)"", ""mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)"", ""FG syndrome 1"""	TNRC11, FGS1		9225980, 10198638, 17334363, 20507344	Standard	NM_005120		Approved	CAGH45, HOPA, OPA1, TRAP230, KIAA0192, OKS	uc004dyy.3	Q93074	OTTHUMG00000021788	ENST00000374080.3:c.6149_6151delAGC	X.37:g.70360598_70360600delAGC	ENSP00000363193:p.Gln2076del					MED12_ENST00000374080.3_In_Frame_Del_p.EQ2050del|MED12_ENST00000478889.1_3'UTR|MED12_ENST00000374102.1_In_Frame_Del_p.EQ2049del	p.EQ2053del	NM_005120.2	NP_005111.2	Q93074	MED12_HUMAN			42	6357_6359	+	Renal(35;0.156)		2050			Gln-rich.		O15410|O75557|Q9UHV6|Q9UND7	In_Frame_Del	DEL	ENST00000374080.3	37	c.6158_6160delAGC	CCDS43970.1																																																																																				0.586	MED12-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057105.1	NM_005120		7	634						7	634	---	---	---	---
ZBTB33	10009	broad.mit.edu	37	X	119388276	119388278	+	In_Frame_Del	DEL	GAT	GAT	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chrX:119388276_119388278delGAT	ENST00000326624.2	+	2	1234_1236	c.1006_1008delGAT	c.(1006-1008)gatdel	p.D340del	ZBTB33_ENST00000557385.1_In_Frame_Del_p.D340del	NM_006777.3	NP_006768.1	Q86T24	KAISO_HUMAN	zinc finger and BTB domain containing 33	340					intracellular signal transduction (GO:0035556)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|methyl-CpG binding (GO:0008327)|sequence-specific DNA binding (GO:0043565)			breast(2)|central_nervous_system(2)|endometrium(6)|large_intestine(6)|lung(5)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	26						GGAAATAATAGATGATGATGATG	0.433																																						ENST00000326624.2																			0				breast(2)|central_nervous_system(2)|endometrium(6)|large_intestine(6)|lung(5)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	26						c.(1006-1008)del		zinc finger and BTB domain containing 33																																				SO:0001651	inframe_deletion	10009				intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent|Wnt receptor signaling pathway	cytoplasm|nucleolus|plasma membrane	DNA binding|protein binding|zinc ion binding	g.chrX:119388276_119388278delGAT	BC042753	CCDS14596.1	Xq23	2013-01-09			ENSG00000177485	ENSG00000177485		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	16682	protein-coding gene	gene with protein product		300329					Standard	NM_001184742		Approved	ZNF-kaiso, kaiso, WUGSC:H_DJ525N14.1, KAISO, ZNF348	uc004esn.1	Q86T24	OTTHUMG00000171159	ENST00000326624.2:c.1006_1008delGAT	X.37:g.119388285_119388287delGAT	ENSP00000314153:p.Asp340del					ZBTB33_ENST00000557385.1_In_Frame_Del_p.D340del	p.D340del	NM_006777.3	NP_006768.1	Q86T24	KAISO_HUMAN			2	1234_1236	+			340					B2R5U6|O00319|Q7Z361|Q8IVP6|Q8N3P0	In_Frame_Del	DEL	ENST00000326624.2	37	c.1006_1008delGAT	CCDS14596.1																																																																																				0.433	ZBTB33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058085.2	NM_006777		10	871						10	871	---	---	---	---
HTATSF1	27336	broad.mit.edu	37	X	135585048	135585050	+	In_Frame_Del	DEL	AAG	AAG	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chrX:135585048_135585050delAAG	ENST00000218364.4	+	5	856_858	c.682_684delAAG	c.(682-684)aagdel	p.K232del	HTATSF1_ENST00000535601.1_In_Frame_Del_p.K232del	NM_014500.4	NP_055315.2	O43719	HTSF1_HUMAN	HIV-1 Tat specific factor 1	232	Poly-Lys.				regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(14)|ovary(3)|prostate(1)	30	Acute lymphoblastic leukemia(192;0.000127)					TGATGCCTCAAAGAAGAAGAAGA	0.335																																						ENST00000535601.1																			0				NS(1)|biliary_tract(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(14)|ovary(3)|prostate(1)	30						c.(682-684)del		HIV-1 Tat specific factor 1																																				SO:0001651	inframe_deletion	27336				regulation of transcription elongation, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent|viral genome replication	nucleus	nucleotide binding|protein binding|RNA binding	g.chrX:135585048_135585050delAAG	U76992	CCDS14657.1	Xq26.3	2013-02-12	2006-01-09		ENSG00000102241	ENSG00000102241		"""RNA binding motif (RRM) containing"""	5276	protein-coding gene	gene with protein product		300346	"""HIV TAT specific factor 1"""			8849451	Standard	NM_014500		Approved	TAT-SF1	uc004ezx.3	O43719	OTTHUMG00000022510	ENST00000218364.4:c.682_684delAAG	X.37:g.135585057_135585059delAAG	ENSP00000218364:p.Lys232del					HTATSF1_ENST00000218364.4_In_Frame_Del_p.K232del	p.K232del	NM_001163280.1	NP_001156752.1	O43719	HTSF1_HUMAN			6	1104_1106	+	Acute lymphoblastic leukemia(192;0.000127)		232			Poly-Lys.		D3DWG9|Q59G06|Q99730	In_Frame_Del	DEL	ENST00000218364.4	37	c.682_684delAAG	CCDS14657.1																																																																																				0.335	HTATSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058497.1	NM_014500		7	602						7	602	---	---	---	---
CXorf66	347487	broad.mit.edu	37	X	139038599	139038599	+	Frame_Shift_Del	DEL	T	T	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chrX:139038599delT	ENST00000370540.1	-	3	565	c.542delA	c.(541-543)aagfs	p.K181fs		NM_001013403.2	NP_001013421.1	Q5JRM2	CX066_HUMAN	chromosome X open reading frame 66	181						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(13)|skin(1)|stomach(1)	26						CTTATGTGCCTTTTCCAGGTG	0.413																																						ENST00000370540.1																			0				breast(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(13)|skin(1)|stomach(1)	26						c.(541-543)agfs		chromosome X open reading frame 66							268.0	240.0	249.0					X																	139038599		2203	4300	6503	SO:0001589	frameshift_variant	347487					integral to membrane		g.chrX:139038599delT		CCDS35411.1	Xq27.1	2014-05-30			ENSG00000203933	ENSG00000203933			33743	protein-coding gene	gene with protein product	"""secreted glycoprotein, X-linked"""					24709545	Standard	NM_001013403		Approved	RP11-35F15.2, SGPX	uc004fbb.3	Q5JRM2	OTTHUMG00000022539	ENST00000370540.1:c.542delA	X.37:g.139038599delT	ENSP00000359571:p.Lys181fs						p.K181fs	NM_001013403.2	NP_001013421.1	Q5JRM2	CX066_HUMAN			3	565	-			181						Frame_Shift_Del	DEL	ENST00000370540.1	37	c.542delA	CCDS35411.1																																																																																				0.413	CXorf66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058572.1	NM_001013403		8	1872						8	1872	---	---	---	---
MAMLD1	10046	broad.mit.edu	37	X	149639325	149639327	+	In_Frame_Del	DEL	CAG	CAG	-	rs374739932|rs374561693		TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chrX:149639325_149639327delCAG	ENST00000370401.2	+	4	1790_1792	c.1480_1482delCAG	c.(1480-1482)cagdel	p.Q502del	MAMLD1_ENST00000426613.2_In_Frame_Del_p.Q477del|MAMLD1_ENST00000455522.2_5'UTR|MAMLD1_ENST00000432680.2_In_Frame_Del_p.Q477del|MAMLD1_ENST00000262858.5_In_Frame_Del_p.Q502del			Q13495	MAMD1_HUMAN	mastermind-like domain containing 1	502	Poly-Gln.				male gonad development (GO:0008584)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)		p.Q469Q(1)|p.Q494Q(1)|p.Q421Q(1)		breast(1)|endometrium(4)|kidney(3)|large_intestine(12)|lung(14)|ovary(1)|prostate(2)	37	Acute lymphoblastic leukemia(192;6.56e-05)					AAGCcagcaacagcagcagcagc	0.532																																						ENST00000370401.2																			3	Substitution - coding silent(3)	p.Q469Q(1)|p.Q494Q(1)|p.Q421Q(1)	kidney(3)	breast(1)|endometrium(4)|kidney(3)|large_intestine(12)|lung(14)|ovary(1)|prostate(2)	37						c.(1480-1482)del		mastermind-like domain containing 1																																				SO:0001651	inframe_deletion	10046				male gonad development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus		g.chrX:149639325_149639327delCAG	U46023	CCDS14693.2, CCDS55525.1, CCDS55526.1	Xq28	2008-02-05	2008-01-03	2008-01-03	ENSG00000013619	ENSG00000013619			2568	protein-coding gene	gene with protein product		300120	"""chromosome X open reading frame 6"""	CXorf6		9169146, 17086185, 18162467	Standard	NM_001177465		Approved	CG1, F18	uc011mxu.2	Q13495	OTTHUMG00000024157	ENST00000370401.2:c.1480_1482delCAG	X.37:g.149639334_149639336delCAG	ENSP00000359428:p.Gln502del					MAMLD1_ENST00000455522.2_5'UTR|MAMLD1_ENST00000432680.2_In_Frame_Del_p.Q477del|MAMLD1_ENST00000426613.2_In_Frame_Del_p.Q477del|MAMLD1_ENST00000262858.5_In_Frame_Del_p.Q502del	p.Q502del			Q13495	MAMD1_HUMAN			4	1790_1792	+	Acute lymphoblastic leukemia(192;6.56e-05)		502			Poly-Gln.		B2RCQ4|B4DG93|B9EGA5	In_Frame_Del	DEL	ENST00000370401.2	37	c.1480_1482delCAG	CCDS14693.2																																																																																				0.532	MAMLD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060844.2	NM_005491		13	524						13	524	---	---	---	---
PASD1	139135	broad.mit.edu	37	X	150817142	150817144	+	In_Frame_Del	DEL	GCT	GCT	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chrX:150817142_150817144delGCT	ENST00000370357.4	+	9	930_932	c.685_687delGCT	c.(685-687)gctdel	p.A236del		NM_173493.2	NP_775764.2	Q8IV76	PASD1_HUMAN	PAS domain containing 1	236	Poly-Ala.					nucleus (GO:0005634)	signal transducer activity (GO:0004871)	p.A229A(2)		breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(3)|liver(1)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	48	Acute lymphoblastic leukemia(192;6.56e-05)					CGTTGAACCCgctgctgctgctg	0.433																																						ENST00000370357.4																			2	Substitution - coding silent(2)	p.A229A(2)	lung(2)	breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(3)|liver(1)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	48						c.(685-687)del		PAS domain containing 1																																				SO:0001651	inframe_deletion	139135					nucleus	signal transducer activity	g.chrX:150817142_150817144delGCT	AY270020	CCDS35431.1	Xq28	2009-08-06			ENSG00000166049	ENSG00000166049			20686	protein-coding gene	gene with protein product	"""cancer/testis antigen 63"""					15122589, 15162151	Standard	NM_173493		Approved	CT63	uc004fev.4	Q8IV76	OTTHUMG00000024169	ENST00000370357.4:c.685_687delGCT	X.37:g.150817151_150817153delGCT	ENSP00000359382:p.Ala236del						p.A236del	NM_173493.2	NP_775764.2	Q8IV76	PASD1_HUMAN			9	930_932	+	Acute lymphoblastic leukemia(192;6.56e-05)		236			Poly-Ala.		Q3MNE0|Q69HD7|Q8N7X9	In_Frame_Del	DEL	ENST00000370357.4	37	c.685_687delGCT	CCDS35431.1																																																																																				0.433	PASD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060879.2	NM_173493		15	970						15	970	---	---	---	---
MAGEA10	4109	broad.mit.edu	37	X	151303906	151303908	+	In_Frame_Del	DEL	AGG	AGG	-			TCGA-HZ-8638-01A-11D-2396-08	TCGA-HZ-8638-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08f8e370-782c-48de-989b-b861fafa9155	380736fb-bc7c-4d24-b8d8-66441c315ed4	g.chrX:151303906_151303908delAGG	ENST00000370323.4	-	4	501_503	c.185_187delCCT	c.(184-189)tcctgc>tgc	p.S62del	RP11-1007I13.4_ENST00000509345.2_RNA|MAGEA10_ENST00000244096.3_In_Frame_Del_p.S62del	NM_001251828.1|NM_021048.4	NP_001238757.1|NP_066386	P43363	MAGAA_HUMAN	melanoma antigen family A, 10	62	Poly-Ser.					nucleus (GO:0005634)				endometrium(2)|kidney(2)|large_intestine(4)|lung(11)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	23	Acute lymphoblastic leukemia(192;6.56e-05)					AGAGGATAGCaggaggaggagga	0.562																																						ENST00000370323.4																			0				endometrium(2)|kidney(2)|large_intestine(4)|lung(11)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						c.(184-189)tgc>t		melanoma antigen family A, 10																																				SO:0001651	inframe_deletion	4109							g.chrX:151303906_151303908delAGG		CCDS14705.1	Xq28	2009-03-13			ENSG00000124260	ENSG00000124260			6797	protein-coding gene	gene with protein product	"""MAGE-10 antigen"", ""melanoma-associated antigen 10"", ""cancer/testis antigen family 1, member 10"""	300343		MAGE10		8575766	Standard	NM_001011543		Approved	MGC10599, CT1.10	uc004ffl.3	P43363	OTTHUMG00000024180	ENST00000370323.4:c.185_187delCCT	X.37:g.151303915_151303917delAGG	ENSP00000359347:p.Ser62del					RP11-1007I13.4_ENST00000509345.2_RNA|MAGEA10_ENST00000244096.3_In_Frame_Del_p.SC62del	p.SC62del	NM_001251828.1|NM_021048.4	NP_001238757.1|NP_066386.2	P43363	MAGAA_HUMAN			4	501_503	-	Acute lymphoblastic leukemia(192;6.56e-05)		62			Poly-Ser.			In_Frame_Del	DEL	ENST00000370323.4	37	c.185_187delCCT	CCDS14705.1																																																																																				0.562	MAGEA10-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060916.3	NM_021048		9	802						9	802	---	---	---	---
