#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
ZNF335	63925	broad.mit.edu	37	20	44578157	44578157	+	Silent	SNP	T	T	C			TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	c181d15b-c8ae-4d11-b57f-8de22eb27f81	g.chr20:44578157T>C	ENST00000322927.2	-	25	3820	c.3720A>G	c.(3718-3720)gaA>gaG	p.E1240E	ZNF335_ENST00000426788.1_Silent_p.E1085E	NM_022095.3	NP_071378.1	Q9H4Z2	ZN335_HUMAN	zinc finger protein 335	1240	Gln-rich.				brain development (GO:0007420)|brain morphogenesis (GO:0048854)|cerebral cortex neuron differentiation (GO:0021895)|histone H3-K4 trimethylation (GO:0080182)|in utero embryonic development (GO:0001701)|neuron projection morphogenesis (GO:0048812)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of neurogenesis (GO:0050769)|regulation of gene expression, epigenetic (GO:0040029)|regulation of histone H3-K4 methylation (GO:0051569)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(13)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	51		Myeloproliferative disorder(115;0.0122)				CCACAACATATTCCTGGGGGA	0.612																																						ENST00000322927.2																			0				NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(13)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	51						c.(3718-3720)gaA>gaG		zinc finger protein 335							53.0	41.0	45.0					20																	44578157		2203	4300	6503	SO:0001819	synonymous_variant	63925				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr20:44578157T>C	AK026157	CCDS13389.1	20q13.12	2011-09-12			ENSG00000198026	ENSG00000198026		"""Zinc fingers, C2H2-type"""	15807	protein-coding gene	gene with protein product	"""NRC-interacting factor 1"""	610827				12215545, 19131338	Standard	NM_022095		Approved	bA465L10.2, NIF-1	uc002xqw.3	Q9H4Z2	OTTHUMG00000032637	ENST00000322927.2:c.3720A>G	20.37:g.44578157T>C						ZNF335_ENST00000426788.1_Silent_p.E1085E	p.E1240E	NM_022095.3	NP_071378.1	Q9H4Z2	ZN335_HUMAN			25	3820	-		Myeloproliferative disorder(115;0.0122)	1240			Gln-rich.		B4DLG7|Q548D0|Q9H684	Silent	SNP	ENST00000322927.2	37	c.3720A>G	CCDS13389.1																																																																																				0.612	ZNF335-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079553.1	NM_022095		4	21	0	0	0	1	0	4	21				
MT-ND1	4535	broad.mit.edu	37	M	3664	3664	+	Missense_Mutation	SNP	G	G	A			TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	c181d15b-c8ae-4d11-b57f-8de22eb27f81	g.chrM:3664G>A	ENST00000361390.2	+	1	358	c.358G>A	c.(358-360)Ggg>Agg	p.G120R	MT-TV_ENST00000387342.1_RNA|MT-TN_ENST00000387400.1_RNA|MT-TY_ENST00000387409.1_RNA|MT-ND2_ENST00000361453.3_5'Flank|MT-TC_ENST00000387405.1_RNA|MT-TA_ENST00000387392.1_RNA|MT-TL1_ENST00000386347.1_RNA|MT-TM_ENST00000387377.1_RNA|MT-RNR1_ENST00000389680.2_RNA|MT-TQ_ENST00000387372.1_RNA|MT-CO1_ENST00000361624.2_5'Flank|MT-TI_ENST00000387365.1_RNA|MT-RNR2_ENST00000387347.2_RNA|MT-TW_ENST00000387382.1_RNA			P03886	NU1M_HUMAN	mitochondrially encoded NADH dehydrogenase 1	120					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|endometrium(13)|kidney(17)|lung(2)|prostate(1)	34					Desflurane(DB01189)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	TCCTCTGATCAGGGTGAGCAT	0.512																																						ENST00000361390.2																			0				breast(1)|endometrium(13)|kidney(17)|lung(2)|prostate(1)	34						c.(358-360)Ggg>Agg		mitochondrially encoded NADH dehydrogenase 1																																				SO:0001583	missense	4535							g.chrM:3664G>A			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198888	ENSG00000198888	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7455	protein-coding gene	gene with protein product	"""complex I ND1 subunit"", ""NADH-ubiquinone oxidoreductase chain 1"""	516000	"""NADH dehydrogenase 1"""	MTND1			Standard			Approved	ND1, NAD1		P03886		ENST00000361390.2:c.358G>A	M.37:g.3664G>A	ENSP00000354687:p.Gly120Arg						p.120_120insR							1	358	+								C0JKH6|Q37523	Missense_Mutation	SNP	ENST00000361390.2	37	c.358G>A																																																																																					0.512	MT-ND1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024026		16	2	0	0	0	1	0	16	2				
FAM101A	144347	broad.mit.edu	37	12	124798816	124798816	+	Silent	SNP	G	G	A	rs77570261	byFrequency	TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	c181d15b-c8ae-4d11-b57f-8de22eb27f81	g.chr12:124798816G>A	ENST00000389727.3	+	3	396	c.396G>A	c.(394-396)acG>acA	p.T132T	FAM101A_ENST00000338359.4_Silent_p.T51T|FAM101A_ENST00000324038.3_Silent_p.T51T|FAM101A_ENST00000546355.1_Silent_p.T51T			Q6ZTI6	F101A_HUMAN	family with sequence similarity 101, member A	132										endometrium(1)|kidney(1)|lung(1)	3	all_neural(191;0.101)|Medulloblastoma(191;0.163)			Epithelial(86;2.38e-05)|OV - Ovarian serous cystadenocarcinoma(86;6.95e-05)|all cancers(50;0.000361)|BRCA - Breast invasive adenocarcinoma(302;0.059)		CCACCGTCACGGCCTACAGCG	0.642													G|||	7	0.00139776	0.0	0.0	5008	,	,		19308	0.0069		0.0	False		,,,				2504	0.0					ENST00000389727.3																			0				endometrium(1)|kidney(1)|lung(1)	3						c.(394-396)acG>acA		family with sequence similarity 101, member A							96.0	83.0	88.0					12																	124798816		2203	4300	6503	SO:0001819	synonymous_variant	144347							g.chr12:124798816G>A		CCDS9258.1	12q24.31	2012-11-30			ENSG00000178882	ENSG00000178882			27051	protein-coding gene	gene with protein product		615927				12477932	Standard	NM_181709		Approved	FLJ44614	uc001ugd.2	Q6ZTI6	OTTHUMG00000168609	ENST00000389727.3:c.396G>A	12.37:g.124798816G>A						FAM101A_ENST00000546355.1_Silent_p.T51T|FAM101A_ENST00000324038.3_Silent_p.T51T|FAM101A_ENST00000338359.4_Silent_p.T51T	p.T132T			Q6ZTI6	F101A_HUMAN		Epithelial(86;2.38e-05)|OV - Ovarian serous cystadenocarcinoma(86;6.95e-05)|all cancers(50;0.000361)|BRCA - Breast invasive adenocarcinoma(302;0.059)	3	396	+	all_neural(191;0.101)|Medulloblastoma(191;0.163)		132					A5D8T5	Silent	SNP	ENST00000389727.3	37	c.396G>A																																																																																					0.642	FAM101A-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_181709		17	147	0	0	0	1	0	17	147				
FLG	2312	broad.mit.edu	37	1	152286555	152286555	+	Silent	SNP	A	A	C			TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	c181d15b-c8ae-4d11-b57f-8de22eb27f81	g.chr1:152286555A>C	ENST00000368799.1	-	3	842	c.807T>G	c.(805-807)tcT>tcG	p.S269S	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	269	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGTTCACTTGAGATGATGATT	0.423									Ichthyosis																													ENST00000368799.1																			0				autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424						c.(805-807)tcT>tcG		filaggrin							244.0	247.0	246.0					1																	152286555		2203	4300	6503	SO:0001819	synonymous_variant	2312	Ichthyosis	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity	g.chr1:152286555A>C	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.807T>G	1.37:g.152286555A>C						FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000392688.2_RNA	p.S269S	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	LUSC - Lung squamous cell carcinoma(543;0.206)		3	842	-	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		269			Ser-rich.		Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	37	c.807T>G	CCDS30860.1																																																																																				0.423	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		10	125	0	0	0	1	0	10	125				
RBP3	5949	broad.mit.edu	37	10	48390034	48390034	+	Missense_Mutation	SNP	C	C	T			TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	c181d15b-c8ae-4d11-b57f-8de22eb27f81	g.chr10:48390034C>T	ENST00000224600.4	-	1	957	c.844G>A	c.(844-846)Gtg>Atg	p.V282M	AL731561.2_ENST00000581861.1_RNA	NM_002900.2	NP_002891.1	P10745	RET3_HUMAN	retinol binding protein 3, interstitial	282	4 X approximate tandem repeats.		V -> M. {ECO:0000269|PubMed:19074801}.		lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transport (GO:0006810)|visual perception (GO:0007601)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|interphotoreceptor matrix (GO:0033165)|vesicle (GO:0031982)	retinal binding (GO:0016918)|retinoid binding (GO:0005501)|retinol binding (GO:0019841)|serine-type peptidase activity (GO:0008236)			central_nervous_system(3)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(30)|ovary(1)|prostate(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59					Vitamin A(DB00162)	GACCTGGACACGGGCACCGTG	0.697																																						ENST00000224600.4																			0				central_nervous_system(3)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(30)|ovary(1)|prostate(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59						c.(844-846)Gtg>Atg		retinol binding protein 3, interstitial	Vitamin A(DB00162)						26.0	24.0	25.0					10																	48390034		2202	4300	6502	SO:0001583	missense	5949				lipid metabolic process|proteolysis|transport|visual perception	interphotoreceptor matrix	retinal binding|serine-type peptidase activity	g.chr10:48390034C>T	M22453	CCDS73119.1	10q11.2	2014-05-06	2001-11-28		ENSG00000107618	ENSG00000265203			9921	protein-coding gene	gene with protein product		180290	"""retinol-binding protein 3, interstitial"""				Standard	NM_002900		Approved	D10S64, D10S65, D10S66, RP66	uc001jez.3	P10745	OTTHUMG00000188321	ENST00000224600.4:c.844G>A	10.37:g.48390034C>T	ENSP00000224600:p.Val282Met						p.V282M	NM_002900.2	NP_002891.1	P10745	RET3_HUMAN			1	957	-			282			4 X approximate tandem repeats.		Q0QD34|Q5VSR0|Q8IXN0	Missense_Mutation	SNP	ENST00000224600.4	37	c.844G>A	CCDS7218.1	.	.	.	.	.	.	.	.	.	.	C	16.30	3.085598	0.55861	.	.	ENSG00000107618	ENST00000224600	T	0.65732	-0.17	5.56	5.56	0.83823	Interphotoreceptor retinol-binding (2);	0.242826	0.42548	D	0.000695	T	0.81669	0.4871	M	0.83774	2.66	0.45747	D	0.99864	D	0.89917	1.0	D	0.91635	0.999	D	0.83964	0.0323	10	0.87932	D	0	-35.7589	18.5233	0.90962	0.0:1.0:0.0:0.0	.	282	P10745	RET3_HUMAN	M	282	ENSP00000224600:V282M	ENSP00000224600:V282M	V	-	1	0	RBP3	48010040	0.986000	0.35501	0.959000	0.39883	0.652000	0.38707	2.801000	0.47908	2.640000	0.89533	0.655000	0.94253	GTG		0.697	RBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047888.1	NM_002900		4	46	0	0	0	1	0	4	46				
MLLT3	4300	broad.mit.edu	37	9	20414343	20414343	+	Silent	SNP	A	A	G	rs372894655	byFrequency	TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	c181d15b-c8ae-4d11-b57f-8de22eb27f81	g.chr9:20414343A>G	ENST00000380338.4	-	5	787	c.501T>C	c.(499-501)agT>agC	p.S167S	MLLT3_ENST00000475957.1_5'UTR|MLLT3_ENST00000355930.6_5'UTR|MLLT3_ENST00000429426.2_Silent_p.S164S	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_ENST00000429426.2_Silent_p.S164S|MLLT3_ENST00000355930.6_5'UTR	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		6	54	0	0	0	1	0	6	54				
RUNX2	860	broad.mit.edu	37	6	45390463	45390463	+	Silent	SNP	G	G	A			TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	c181d15b-c8ae-4d11-b57f-8de22eb27f81	g.chr6:45390463G>A	ENST00000371438.1	+	2	550	c.192G>A	c.(190-192)caG>caA	p.Q64Q	RUNX2_ENST00000576263.1_Silent_p.Q64Q|RUNX2_ENST00000465038.2_Silent_p.Q64Q|RUNX2_ENST00000352853.5_Silent_p.Q132Q|RUNX2_ENST00000359524.5_Silent_p.Q50Q|RUNX2_ENST00000371436.6_Silent_p.Q64Q|RUNX2_ENST00000541979.1_Silent_p.Q132Q|RP1-244F24.1_ENST00000606796.1_RNA|RUNX2_ENST00000371432.3_Silent_p.Q50Q	NM_001024630.3	NP_001019801.3	Q13950	RUNX2_HUMAN	runt-related transcription factor 2	64	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						agcagcagcagcaacagcagc	0.736																																						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.(190-192)caG>caA		runt-related transcription factor 2							11.0	16.0	14.0					6																	45390463		1448	3096	4544	SO:0001819	synonymous_variant	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.chr6:45390463G>A	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.192G>A	6.37:g.45390463G>A						RUNX2_ENST00000465038.2_Silent_p.Q64Q|RUNX2_ENST00000371436.6_Silent_p.Q64Q|RUNX2_ENST00000352853.5_Silent_p.Q132Q|RUNX2_ENST00000359524.5_Silent_p.Q50Q|RUNX2_ENST00000371432.3_Silent_p.Q50Q|RUNX2_ENST00000541979.1_Silent_p.Q132Q|RUNX2_ENST00000576263.1_Silent_p.Q64Q	p.Q64Q	NM_001024630.3	NP_001019801.3	Q13950	RUNX2_HUMAN			2	550	+			64			Poly-Gln.		O14614|O14615|O95181	Silent	SNP	ENST00000371438.1	37	c.192G>A	CCDS43467.2																																																																																				0.736	RUNX2-003	KNOWN	not_organism_supported|upstream_ATG|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040755.2	NM_004348		5	57	0	0	0	1	0	5	57				
CABYR	26256	broad.mit.edu	37	18	21736278	21736278	+	Silent	SNP	T	T	A	rs150107485	byFrequency	TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	c181d15b-c8ae-4d11-b57f-8de22eb27f81	g.chr18:21736278T>A	ENST00000399481.2	+	2	671	c.519T>A	c.(517-519)ccT>ccA	p.P173P	CABYR_ENST00000399499.1_Intron|CABYR_ENST00000415309.2_Intron|CABYR_ENST00000327201.6_Intron|CABYR_ENST00000581397.1_Intron|CABYR_ENST00000399496.3_Intron			O75952	CABYR_HUMAN	calcium binding tyrosine-(Y)-phosphorylation regulated	271					epithelial cilium movement (GO:0003351)|sperm capacitation (GO:0048240)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|motile cilium (GO:0031514)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)	calcium ion binding (GO:0005509)|enzyme binding (GO:0019899)|protein heterodimerization activity (GO:0046982)|SH3 domain binding (GO:0017124)			breast(1)|endometrium(2)|large_intestine(4)|lung(4)	11	all_cancers(21;9.13e-05)|all_epithelial(16;5.49e-07)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0305)|Ovarian(20;0.17)					AAGAACCTCCTGCTTATGATC	0.438													T|||	8	0.00159744	0.0	0.0058	5008	,	,		22315	0.0		0.003	False		,,,				2504	0.001					ENST00000399481.2																			0				breast(1)|endometrium(2)|large_intestine(4)|lung(4)	11						c.(517-519)ccT>ccA		calcium binding tyrosine-(Y)-phosphorylation regulated		T	,,,,,	2,4404	4.2+/-10.8	0,2,2201	84.0	78.0	80.0		813,,,759,,	4.8	1.0	18	dbSNP_134	80	19,8581	14.0+/-48.4	0,19,4281	no	coding-synonymous,intron,intron,coding-synonymous,intron,intron	CABYR	NM_012189.2,NM_138643.1,NM_138644.1,NM_153768.1,NM_153769.1,NM_153770.1	,,,,,	0,21,6482	AA,AT,TT		0.2209,0.0454,0.1615	,,,,,	271/494,,,253/476,,	21736278	21,12985	2203	4300	6503	SO:0001819	synonymous_variant	26256				ciliary or flagellar motility|signal transduction|sperm capacitation	cytoplasm|cytoskeleton|flagellum|motile cilium|nucleus	calcium ion binding|cAMP-dependent protein kinase regulator activity|enzyme binding|protein heterodimerization activity|SH3 domain binding	g.chr18:21736278T>A	AF088868	CCDS11881.1, CCDS11882.1, CCDS11883.1, CCDS42420.1, CCDS45840.1	18q11.2	2009-08-06	2007-11-22		ENSG00000154040	ENSG00000154040			15569	protein-coding gene	gene with protein product	"""fibrousheathin 2"", ""cancer/testis antigen 88"""	612135				11820818, 17317841, 16139264	Standard	NM_012189		Approved	FSP-2, CBP86, CT88	uc002kux.3	O75952	OTTHUMG00000037365	ENST00000399481.2:c.519T>A	18.37:g.21736278T>A						CABYR_ENST00000399499.1_Intron|CABYR_ENST00000581397.1_Intron|CABYR_ENST00000327201.6_Intron|CABYR_ENST00000415309.2_Intron|CABYR_ENST00000399496.3_Intron	p.P173P			O75952	CABYR_HUMAN			2	671	+	all_cancers(21;9.13e-05)|all_epithelial(16;5.49e-07)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0305)|Ovarian(20;0.17)		271					B2R857|Q8WXW5|Q9HAY3|Q9HAY4|Q9HAY5|Q9HCY9	Silent	SNP	ENST00000399481.2	37	c.519T>A																																																																																					0.438	CABYR-201	KNOWN	basic	protein_coding	protein_coding		NM_153770		4	37	0	0	0	1	0	4	37				
ITGB7	3695	broad.mit.edu	37	12	53586181	53586181	+	Silent	SNP	C	C	T			TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	c181d15b-c8ae-4d11-b57f-8de22eb27f81	g.chr12:53586181C>T	ENST00000267082.5	-	14	2319	c.2088G>A	c.(2086-2088)caG>caA	p.Q696Q	ITGB7_ENST00000338737.4_Silent_p.Q548Q|ITGB7_ENST00000550743.2_Silent_p.Q548Q|ITGB7_ENST00000422257.3_Silent_p.Q696Q	NM_000889.1	NP_000880.1	P26010	ITB7_HUMAN	integrin, beta 7	696					cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|cell-matrix adhesion involved in ameboidal cell migration (GO:0003366)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte tethering or rolling (GO:0050901)|multicellular organismal development (GO:0007275)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|substrate adhesion-dependent cell spreading (GO:0034446)|T cell migration (GO:0072678)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alpha4-beta7 complex (GO:0034669)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)|virus receptor activity (GO:0001618)			NS(2)|breast(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(3)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						AGAAGAACAGCTGGTTGTCCA	0.567																																						ENST00000267082.5																			0				NS(2)|breast(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(3)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						c.(2086-2088)caG>caA		integrin, beta 7							140.0	125.0	130.0					12																	53586181		2203	4300	6503	SO:0001819	synonymous_variant	3695				cell-matrix adhesion|integrin-mediated signaling pathway|multicellular organismal development|regulation of immune response	integrin complex	identical protein binding|metal ion binding|receptor activity	g.chr12:53586181C>T		CCDS8849.1	12q13.1	2010-03-23				ENSG00000139626		"""Integrins"""	6162	protein-coding gene	gene with protein product		147559				2040616	Standard	XM_005268851		Approved		uc001scc.3	P26010		ENST00000267082.5:c.2088G>A	12.37:g.53586181C>T						ITGB7_ENST00000338737.4_Silent_p.Q548Q|ITGB7_ENST00000550743.2_Silent_p.Q548Q|ITGB7_ENST00000422257.3_Silent_p.Q696Q	p.Q696Q	NM_000889.1	NP_000880.1	P26010	ITB7_HUMAN			14	2319	-			696					Q9UCP7|Q9UCS7	Silent	SNP	ENST00000267082.5	37	c.2088G>A	CCDS8849.1																																																																																				0.567	ITGB7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405821.2			13	81	0	0	0	1	0	13	81				
ACOT1	641371	broad.mit.edu	37	14	74008372	74008372	+	Silent	SNP	T	T	C	rs371750964	byFrequency	TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	c181d15b-c8ae-4d11-b57f-8de22eb27f81	g.chr14:74008372T>C	ENST00000311148.4	+	2	941	c.633T>C	c.(631-633)gcT>gcC	p.A211A	HEATR4_ENST00000560393.1_Intron|HEATR4_ENST00000334988.2_Intron|ACOT1_ENST00000557556.1_Silent_p.A211A|HEATR4_ENST00000553558.1_Intron	NM_001037161.1	NP_001032238.1	Q86TX2	ACOT1_HUMAN	acyl-CoA thioesterase 1	211					acyl-CoA metabolic process (GO:0006637)|long-chain fatty acid metabolic process (GO:0001676)|very long-chain fatty acid metabolic process (GO:0000038)	cytosol (GO:0005829)	acyl-CoA hydrolase activity (GO:0047617)|carboxylic ester hydrolase activity (GO:0052689)|palmitoyl-CoA hydrolase activity (GO:0016290)			endometrium(1)|large_intestine(1)|lung(2)	4				OV - Ovarian serous cystadenocarcinoma(108;1.37e-45)|BRCA - Breast invasive adenocarcinoma(234;0.0033)		TTGAAGAAGCTGTGAACTACT	0.458													-|||	65	0.0129792	0.0257	0.0115	5008	,	,		10110	0.002		0.0139	False		,,,				2504	0.0072					ENST00000311148.4																			0				endometrium(1)|large_intestine(1)|lung(2)	4						c.(631-633)gcT>gcC		acyl-CoA thioesterase 1																																				SO:0001819	synonymous_variant	641371							g.chr14:74008372T>C	DQ082754	CCDS32117.1	14q24.3	2013-09-20			ENSG00000184227	ENSG00000184227		"""Acyl CoA thioesterases"""	33128	protein-coding gene	gene with protein product		614313				16103133, 16940157	Standard	NM_001037161		Approved	ACH2, CTE-1, LACH2		Q86TX2	OTTHUMG00000171607	ENST00000311148.4:c.633T>C	14.37:g.74008372T>C						HEATR4_ENST00000334988.2_Intron|HEATR4_ENST00000560393.1_Intron|HEATR4_ENST00000553558.1_Intron|ACOT1_ENST00000557556.1_Silent_p.A211A	p.A211A	NM_001037161.1	NP_001032238.1				OV - Ovarian serous cystadenocarcinoma(108;1.37e-45)|BRCA - Breast invasive adenocarcinoma(234;0.0033)	2	941	+								A1L173|Q3I5F9	Silent	SNP	ENST00000311148.4	37	c.633T>C	CCDS32117.1																																																																																				0.458	ACOT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414432.1	NM_001037161		4	47	0	0	0	1	0	4	47				
ZNF335	63925	broad.mit.edu	37	20	44578157	44578157	+	Silent	SNP	T	T	C			TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	d6d2a21b-6095-4ec9-8254-e5d2564aad50	g.chr20:44578157T>C	ENST00000322927.2	-	25	3820	c.3720A>G	c.(3718-3720)gaA>gaG	p.E1240E	ZNF335_ENST00000426788.1_Silent_p.E1085E	NM_022095.3	NP_071378.1	Q9H4Z2	ZN335_HUMAN	zinc finger protein 335	1240	Gln-rich.				brain development (GO:0007420)|brain morphogenesis (GO:0048854)|cerebral cortex neuron differentiation (GO:0021895)|histone H3-K4 trimethylation (GO:0080182)|in utero embryonic development (GO:0001701)|neuron projection morphogenesis (GO:0048812)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of neurogenesis (GO:0050769)|regulation of gene expression, epigenetic (GO:0040029)|regulation of histone H3-K4 methylation (GO:0051569)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(13)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	51		Myeloproliferative disorder(115;0.0122)				CCACAACATATTCCTGGGGGA	0.612																																						ENST00000322927.2																			0				NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(13)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	51						c.(3718-3720)gaA>gaG		zinc finger protein 335							53.0	41.0	45.0					20																	44578157		2203	4300	6503	SO:0001819	synonymous_variant	63925				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr20:44578157T>C	AK026157	CCDS13389.1	20q13.12	2011-09-12			ENSG00000198026	ENSG00000198026		"""Zinc fingers, C2H2-type"""	15807	protein-coding gene	gene with protein product	"""NRC-interacting factor 1"""	610827				12215545, 19131338	Standard	NM_022095		Approved	bA465L10.2, NIF-1	uc002xqw.3	Q9H4Z2	OTTHUMG00000032637	ENST00000322927.2:c.3720A>G	20.37:g.44578157T>C						ZNF335_ENST00000426788.1_Silent_p.E1085E	p.E1240E	NM_022095.3	NP_071378.1	Q9H4Z2	ZN335_HUMAN			25	3820	-		Myeloproliferative disorder(115;0.0122)	1240			Gln-rich.		B4DLG7|Q548D0|Q9H684	Silent	SNP	ENST00000322927.2	37	c.3720A>G	CCDS13389.1																																																																																				0.612	ZNF335-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079553.1	NM_022095		4	21	0	0	0	1	0	4	21				
RUNX2	860	broad.mit.edu	37	6	45390463	45390463	+	Silent	SNP	G	G	A			TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	d6d2a21b-6095-4ec9-8254-e5d2564aad50	g.chr6:45390463G>A	ENST00000371438.1	+	2	550	c.192G>A	c.(190-192)caG>caA	p.Q64Q	RUNX2_ENST00000576263.1_Silent_p.Q64Q|RUNX2_ENST00000465038.2_Silent_p.Q64Q|RUNX2_ENST00000352853.5_Silent_p.Q132Q|RUNX2_ENST00000359524.5_Silent_p.Q50Q|RUNX2_ENST00000371436.6_Silent_p.Q64Q|RUNX2_ENST00000541979.1_Silent_p.Q132Q|RP1-244F24.1_ENST00000606796.1_RNA|RUNX2_ENST00000371432.3_Silent_p.Q50Q	NM_001024630.3	NP_001019801.3	Q13950	RUNX2_HUMAN	runt-related transcription factor 2	64	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						agcagcagcagcaacagcagc	0.736																																						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.(190-192)caG>caA		runt-related transcription factor 2							11.0	16.0	14.0					6																	45390463		1448	3096	4544	SO:0001819	synonymous_variant	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.chr6:45390463G>A	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.192G>A	6.37:g.45390463G>A						RUNX2_ENST00000465038.2_Silent_p.Q64Q|RUNX2_ENST00000541979.1_Silent_p.Q132Q|RUNX2_ENST00000576263.1_Silent_p.Q64Q|RUNX2_ENST00000371432.3_Silent_p.Q50Q|RUNX2_ENST00000352853.5_Silent_p.Q132Q|RUNX2_ENST00000359524.5_Silent_p.Q50Q|RUNX2_ENST00000371436.6_Silent_p.Q64Q	p.Q64Q	NM_001024630.3	NP_001019801.3	Q13950	RUNX2_HUMAN			2	550	+			64			Poly-Gln.		O14614|O14615|O95181	Silent	SNP	ENST00000371438.1	37	c.192G>A	CCDS43467.2																																																																																				0.736	RUNX2-003	KNOWN	not_organism_supported|upstream_ATG|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040755.2	NM_004348		5	57	0	0	0	1	0	5	57				
FAM101A	144347	broad.mit.edu	37	12	124798816	124798816	+	Silent	SNP	G	G	A	rs77570261	byFrequency	TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	d6d2a21b-6095-4ec9-8254-e5d2564aad50	g.chr12:124798816G>A	ENST00000389727.3	+	3	396	c.396G>A	c.(394-396)acG>acA	p.T132T	FAM101A_ENST00000338359.4_Silent_p.T51T|FAM101A_ENST00000324038.3_Silent_p.T51T|FAM101A_ENST00000546355.1_Silent_p.T51T			Q6ZTI6	F101A_HUMAN	family with sequence similarity 101, member A	132										endometrium(1)|kidney(1)|lung(1)	3	all_neural(191;0.101)|Medulloblastoma(191;0.163)			Epithelial(86;2.38e-05)|OV - Ovarian serous cystadenocarcinoma(86;6.95e-05)|all cancers(50;0.000361)|BRCA - Breast invasive adenocarcinoma(302;0.059)		CCACCGTCACGGCCTACAGCG	0.642													G|||	7	0.00139776	0.0	0.0	5008	,	,		19308	0.0069		0.0	False		,,,				2504	0.0					ENST00000389727.3																			0				endometrium(1)|kidney(1)|lung(1)	3						c.(394-396)acG>acA		family with sequence similarity 101, member A							96.0	83.0	88.0					12																	124798816		2203	4300	6503	SO:0001819	synonymous_variant	144347							g.chr12:124798816G>A		CCDS9258.1	12q24.31	2012-11-30			ENSG00000178882	ENSG00000178882			27051	protein-coding gene	gene with protein product		615927				12477932	Standard	NM_181709		Approved	FLJ44614	uc001ugd.2	Q6ZTI6	OTTHUMG00000168609	ENST00000389727.3:c.396G>A	12.37:g.124798816G>A						FAM101A_ENST00000338359.4_Silent_p.T51T|FAM101A_ENST00000546355.1_Silent_p.T51T|FAM101A_ENST00000324038.3_Silent_p.T51T	p.T132T			Q6ZTI6	F101A_HUMAN		Epithelial(86;2.38e-05)|OV - Ovarian serous cystadenocarcinoma(86;6.95e-05)|all cancers(50;0.000361)|BRCA - Breast invasive adenocarcinoma(302;0.059)	3	396	+	all_neural(191;0.101)|Medulloblastoma(191;0.163)		132					A5D8T5	Silent	SNP	ENST00000389727.3	37	c.396G>A																																																																																					0.642	FAM101A-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_181709		17	147	0	0	0	1	0	17	147				
FLG	2312	broad.mit.edu	37	1	152286555	152286555	+	Silent	SNP	A	A	C			TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	d6d2a21b-6095-4ec9-8254-e5d2564aad50	g.chr1:152286555A>C	ENST00000368799.1	-	3	842	c.807T>G	c.(805-807)tcT>tcG	p.S269S	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	269	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGTTCACTTGAGATGATGATT	0.423									Ichthyosis																													ENST00000368799.1																			0				autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424						c.(805-807)tcT>tcG		filaggrin							244.0	247.0	246.0					1																	152286555		2203	4300	6503	SO:0001819	synonymous_variant	2312	Ichthyosis	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity	g.chr1:152286555A>C	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.807T>G	1.37:g.152286555A>C						FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000593011.1_RNA	p.S269S	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	LUSC - Lung squamous cell carcinoma(543;0.206)		3	842	-	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		269			Ser-rich.		Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	37	c.807T>G	CCDS30860.1																																																																																				0.423	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		10	125	0	0	0	1	0	10	125				
RBP3	5949	broad.mit.edu	37	10	48390034	48390034	+	Missense_Mutation	SNP	C	C	T			TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	d6d2a21b-6095-4ec9-8254-e5d2564aad50	g.chr10:48390034C>T	ENST00000224600.4	-	1	957	c.844G>A	c.(844-846)Gtg>Atg	p.V282M	AL731561.2_ENST00000581861.1_RNA	NM_002900.2	NP_002891.1	P10745	RET3_HUMAN	retinol binding protein 3, interstitial	282	4 X approximate tandem repeats.		V -> M. {ECO:0000269|PubMed:19074801}.		lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transport (GO:0006810)|visual perception (GO:0007601)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|interphotoreceptor matrix (GO:0033165)|vesicle (GO:0031982)	retinal binding (GO:0016918)|retinoid binding (GO:0005501)|retinol binding (GO:0019841)|serine-type peptidase activity (GO:0008236)			central_nervous_system(3)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(30)|ovary(1)|prostate(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59					Vitamin A(DB00162)	GACCTGGACACGGGCACCGTG	0.697																																						ENST00000224600.4																			0				central_nervous_system(3)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(30)|ovary(1)|prostate(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59						c.(844-846)Gtg>Atg		retinol binding protein 3, interstitial	Vitamin A(DB00162)						26.0	24.0	25.0					10																	48390034		2202	4300	6502	SO:0001583	missense	5949				lipid metabolic process|proteolysis|transport|visual perception	interphotoreceptor matrix	retinal binding|serine-type peptidase activity	g.chr10:48390034C>T	M22453	CCDS73119.1	10q11.2	2014-05-06	2001-11-28		ENSG00000107618	ENSG00000265203			9921	protein-coding gene	gene with protein product		180290	"""retinol-binding protein 3, interstitial"""				Standard	NM_002900		Approved	D10S64, D10S65, D10S66, RP66	uc001jez.3	P10745	OTTHUMG00000188321	ENST00000224600.4:c.844G>A	10.37:g.48390034C>T	ENSP00000224600:p.Val282Met						p.V282M	NM_002900.2	NP_002891.1	P10745	RET3_HUMAN			1	957	-			282			4 X approximate tandem repeats.		Q0QD34|Q5VSR0|Q8IXN0	Missense_Mutation	SNP	ENST00000224600.4	37	c.844G>A	CCDS7218.1	.	.	.	.	.	.	.	.	.	.	C	16.30	3.085598	0.55861	.	.	ENSG00000107618	ENST00000224600	T	0.65732	-0.17	5.56	5.56	0.83823	Interphotoreceptor retinol-binding (2);	0.242826	0.42548	D	0.000695	T	0.81669	0.4871	M	0.83774	2.66	0.45747	D	0.99864	D	0.89917	1.0	D	0.91635	0.999	D	0.83964	0.0323	10	0.87932	D	0	-35.7589	18.5233	0.90962	0.0:1.0:0.0:0.0	.	282	P10745	RET3_HUMAN	M	282	ENSP00000224600:V282M	ENSP00000224600:V282M	V	-	1	0	RBP3	48010040	0.986000	0.35501	0.959000	0.39883	0.652000	0.38707	2.801000	0.47908	2.640000	0.89533	0.655000	0.94253	GTG		0.697	RBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047888.1	NM_002900		4	46	0	0	0	1	0	4	46				
SBSN	374897	broad.mit.edu	37	19	36018407	36018407	+	Silent	SNP	T	T	C			TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	d6d2a21b-6095-4ec9-8254-e5d2564aad50	g.chr19:36018407T>C	ENST00000452271.2	-	1	805	c.777A>G	c.(775-777)agA>agG	p.R259R	SBSN_ENST00000518157.1_Intron	NM_001166034.1	NP_001159506.1	Q6UWP8	SBSN_HUMAN	suprabasin	259	Ala/Gly/His-rich.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				large_intestine(5)|lung(6)|ovary(1)|prostate(2)	14	all_lung(56;1.62e-08)|Lung NSC(56;2.47e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			CCTGGCCAAATCTCCCTGCCT	0.627																																						ENST00000452271.2																			0				large_intestine(5)|lung(6)|ovary(1)|prostate(2)	14						c.(775-777)agA>agG		suprabasin							56.0	57.0	57.0					19																	36018407		692	1591	2283	SO:0001819	synonymous_variant	374897					extracellular region		g.chr19:36018407T>C	AY358701	CCDS12464.1, CCDS54253.1	19q13.13	2008-02-05							24950	protein-coding gene	gene with protein product		609969				12228223	Standard	NM_198538		Approved	UNQ698, HLAR698	uc002oad.2	Q6UWP8		ENST00000452271.2:c.777A>G	19.37:g.36018407T>C						SBSN_ENST00000518157.1_Intron	p.R259R	NM_001166034.1	NP_001159506.1	Q6UWP8	SBSN_HUMAN	LUSC - Lung squamous cell carcinoma(66;0.0724)		1	805	-	all_lung(56;1.62e-08)|Lung NSC(56;2.47e-08)|Esophageal squamous(110;0.162)		132					A8K5J0|E9PBV3	Silent	SNP	ENST00000452271.2	37	c.777A>G	CCDS54253.1																																																																																				0.627	SBSN-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109463.3	NM_198538		4	7	0	0	0	1	0	4	7				
BMS1P20	96610	broad.mit.edu	37	22	22657649	22657649	+	RNA	SNP	G	G	A			TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	d6d2a21b-6095-4ec9-8254-e5d2564aad50	g.chr22:22657649G>A	ENST00000426066.1	+	0	61					NR_027293.1				BMS1 pseudogene 20																		GGAAAATCGGGCCCCGATACT	0.512																																						ENST00000426066.1																			0																																																			0							g.chr22:22657649G>A			22q11.22	2013-09-20			ENSG00000236850	ENSG00000236850			49153	pseudogene	pseudogene							Standard	XR_430414		Approved				OTTHUMG00000151046		22.37:g.22657649G>A								NR_027293.1						0	61	+									RNA	SNP	ENST00000426066.1	37																																																																																						0.512	BMS1P20-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000473090.1			4	46	0	0	0	1	0	4	46				
MT-ND1	4535	broad.mit.edu	37	M	3664	3664	+	Missense_Mutation	SNP	G	G	A			TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	d6d2a21b-6095-4ec9-8254-e5d2564aad50	g.chrM:3664G>A	ENST00000361390.2	+	1	358	c.358G>A	c.(358-360)Ggg>Agg	p.G120R	MT-TV_ENST00000387342.1_RNA|MT-TN_ENST00000387400.1_RNA|MT-TY_ENST00000387409.1_RNA|MT-ND2_ENST00000361453.3_5'Flank|MT-TC_ENST00000387405.1_RNA|MT-TA_ENST00000387392.1_RNA|MT-TL1_ENST00000386347.1_RNA|MT-TM_ENST00000387377.1_RNA|MT-RNR1_ENST00000389680.2_RNA|MT-TQ_ENST00000387372.1_RNA|MT-CO1_ENST00000361624.2_5'Flank|MT-TI_ENST00000387365.1_RNA|MT-RNR2_ENST00000387347.2_RNA|MT-TW_ENST00000387382.1_RNA			P03886	NU1M_HUMAN	mitochondrially encoded NADH dehydrogenase 1	120					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|endometrium(13)|kidney(17)|lung(2)|prostate(1)	34					Desflurane(DB01189)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	TCCTCTGATCAGGGTGAGCAT	0.512																																						ENST00000361390.2																			0				breast(1)|endometrium(13)|kidney(17)|lung(2)|prostate(1)	34						c.(358-360)Ggg>Agg		mitochondrially encoded NADH dehydrogenase 1																																				SO:0001583	missense	4535							g.chrM:3664G>A			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198888	ENSG00000198888	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7455	protein-coding gene	gene with protein product	"""complex I ND1 subunit"", ""NADH-ubiquinone oxidoreductase chain 1"""	516000	"""NADH dehydrogenase 1"""	MTND1			Standard			Approved	ND1, NAD1		P03886		ENST00000361390.2:c.358G>A	M.37:g.3664G>A	ENSP00000354687:p.Gly120Arg						p.120_120insR							1	358	+								C0JKH6|Q37523	Missense_Mutation	SNP	ENST00000361390.2	37	c.358G>A																																																																																					0.512	MT-ND1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024026		16	2	0	0	0	1	0	16	2				
VCPIP1	80124	broad.mit.edu	37	8	67579177	67579177	+	Missense_Mutation	SNP	G	G	A			TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	d6d2a21b-6095-4ec9-8254-e5d2564aad50	g.chr8:67579177G>A	ENST00000310421.4	-	1	275	c.17C>T	c.(16-18)cCg>cTg	p.P6L	C8orf44_ENST00000519561.1_5'Flank|C8orf44_ENST00000521889.1_5'Flank|C8orf44-SGK3_ENST00000519289.1_5'Flank	NM_025054.4	NP_079330.2	Q96JH7	VCIP1_HUMAN	valosin containing protein (p97)/p47 complex interacting protein 1	6	Pro-rich.				endoplasmic reticulum membrane fusion (GO:0016320)|Golgi reassembly (GO:0090168)|mitotic nuclear division (GO:0007067)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)	ubiquitin-specific protease activity (GO:0004843)			breast(7)|central_nervous_system(2)|cervix(2)|endometrium(3)|kidney(6)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		Lung NSC(129;0.142)|all_lung(136;0.227)	Epithelial(68;0.000771)|OV - Ovarian serous cystadenocarcinoma(28;0.00248)|all cancers(69;0.00296)|BRCA - Breast invasive adenocarcinoma(89;0.149)			aggcggcggcggcggcggcTG	0.697																																					NSCLC(179;265 2915 6144 43644)	ENST00000310421.4																			0				breast(7)|central_nervous_system(2)|cervix(2)|endometrium(3)|kidney(6)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						c.(16-18)cCg>cTg		valosin containing protein (p97)/p47 complex interacting protein 1							4.0	6.0	6.0					8																	67579177		1743	3670	5413	SO:0001583	missense	80124				protein ubiquitination	endoplasmic reticulum|Golgi stack	ubiquitin-specific protease activity	g.chr8:67579177G>A	AB058753	CCDS6192.1	8q13	2014-02-24			ENSG00000175073	ENSG00000175073		"""OTU domain containing"""	30897	protein-coding gene	gene with protein product		611745				11347906, 12509440	Standard	NM_025054		Approved	VCIP135, KIAA1850, FLJ23132, DUBA3	uc003xwn.3	Q96JH7	OTTHUMG00000164560	ENST00000310421.4:c.17C>T	8.37:g.67579177G>A	ENSP00000309031:p.Pro6Leu						p.P6L	NM_025054.4	NP_079330.2	Q96JH7	VCIP1_HUMAN	Epithelial(68;0.000771)|OV - Ovarian serous cystadenocarcinoma(28;0.00248)|all cancers(69;0.00296)|BRCA - Breast invasive adenocarcinoma(89;0.149)		1	275	-		Lung NSC(129;0.142)|all_lung(136;0.227)	6			Pro-rich.		Q504T4|Q86T93|Q86W01|Q8N3A9|Q9H5R8	Missense_Mutation	SNP	ENST00000310421.4	37	c.17C>T	CCDS6192.1	.	.	.	.	.	.	.	.	.	.	G	14.43	2.532628	0.45073	.	.	ENSG00000175073	ENST00000310421	D	0.87179	-2.22	6.03	6.03	0.97812	.	0.562047	0.17447	N	0.173926	T	0.80979	0.4728	N	0.22421	0.69	0.51482	D	0.999929	B	0.10296	0.003	B	0.04013	0.001	T	0.75388	-0.3335	10	0.87932	D	0	-2.5929	14.9071	0.70727	0.0:0.0:0.8213:0.1787	.	6	Q96JH7	VCIP1_HUMAN	L	6	ENSP00000309031:P6L	ENSP00000309031:P6L	P	-	2	0	VCPIP1	67741731	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.524000	0.53495	2.861000	0.98227	0.655000	0.94253	CCG		0.697	VCPIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379227.1			12	17	0	0	0	1	0	12	17				
CABYR	26256	broad.mit.edu	37	18	21736278	21736278	+	Silent	SNP	T	T	A	rs150107485	byFrequency	TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	d6d2a21b-6095-4ec9-8254-e5d2564aad50	g.chr18:21736278T>A	ENST00000399481.2	+	2	671	c.519T>A	c.(517-519)ccT>ccA	p.P173P	CABYR_ENST00000399499.1_Intron|CABYR_ENST00000415309.2_Intron|CABYR_ENST00000327201.6_Intron|CABYR_ENST00000581397.1_Intron|CABYR_ENST00000399496.3_Intron			O75952	CABYR_HUMAN	calcium binding tyrosine-(Y)-phosphorylation regulated	271					epithelial cilium movement (GO:0003351)|sperm capacitation (GO:0048240)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|motile cilium (GO:0031514)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)	calcium ion binding (GO:0005509)|enzyme binding (GO:0019899)|protein heterodimerization activity (GO:0046982)|SH3 domain binding (GO:0017124)			breast(1)|endometrium(2)|large_intestine(4)|lung(4)	11	all_cancers(21;9.13e-05)|all_epithelial(16;5.49e-07)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0305)|Ovarian(20;0.17)					AAGAACCTCCTGCTTATGATC	0.438													T|||	8	0.00159744	0.0	0.0058	5008	,	,		22315	0.0		0.003	False		,,,				2504	0.001					ENST00000399481.2																			0				breast(1)|endometrium(2)|large_intestine(4)|lung(4)	11						c.(517-519)ccT>ccA		calcium binding tyrosine-(Y)-phosphorylation regulated		T	,,,,,	2,4404	4.2+/-10.8	0,2,2201	84.0	78.0	80.0		813,,,759,,	4.8	1.0	18	dbSNP_134	80	19,8581	14.0+/-48.4	0,19,4281	no	coding-synonymous,intron,intron,coding-synonymous,intron,intron	CABYR	NM_012189.2,NM_138643.1,NM_138644.1,NM_153768.1,NM_153769.1,NM_153770.1	,,,,,	0,21,6482	AA,AT,TT		0.2209,0.0454,0.1615	,,,,,	271/494,,,253/476,,	21736278	21,12985	2203	4300	6503	SO:0001819	synonymous_variant	26256				ciliary or flagellar motility|signal transduction|sperm capacitation	cytoplasm|cytoskeleton|flagellum|motile cilium|nucleus	calcium ion binding|cAMP-dependent protein kinase regulator activity|enzyme binding|protein heterodimerization activity|SH3 domain binding	g.chr18:21736278T>A	AF088868	CCDS11881.1, CCDS11882.1, CCDS11883.1, CCDS42420.1, CCDS45840.1	18q11.2	2009-08-06	2007-11-22		ENSG00000154040	ENSG00000154040			15569	protein-coding gene	gene with protein product	"""fibrousheathin 2"", ""cancer/testis antigen 88"""	612135				11820818, 17317841, 16139264	Standard	NM_012189		Approved	FSP-2, CBP86, CT88	uc002kux.3	O75952	OTTHUMG00000037365	ENST00000399481.2:c.519T>A	18.37:g.21736278T>A						CABYR_ENST00000415309.2_Intron|CABYR_ENST00000399496.3_Intron|CABYR_ENST00000399499.1_Intron|CABYR_ENST00000327201.6_Intron|CABYR_ENST00000581397.1_Intron	p.P173P			O75952	CABYR_HUMAN			2	671	+	all_cancers(21;9.13e-05)|all_epithelial(16;5.49e-07)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0305)|Ovarian(20;0.17)		271					B2R857|Q8WXW5|Q9HAY3|Q9HAY4|Q9HAY5|Q9HCY9	Silent	SNP	ENST00000399481.2	37	c.519T>A																																																																																					0.438	CABYR-201	KNOWN	basic	protein_coding	protein_coding		NM_153770		4	37	0	0	0	1	0	4	37				
ITGB7	3695	broad.mit.edu	37	12	53586181	53586181	+	Silent	SNP	C	C	T			TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	d6d2a21b-6095-4ec9-8254-e5d2564aad50	g.chr12:53586181C>T	ENST00000267082.5	-	14	2319	c.2088G>A	c.(2086-2088)caG>caA	p.Q696Q	ITGB7_ENST00000338737.4_Silent_p.Q548Q|ITGB7_ENST00000550743.2_Silent_p.Q548Q|ITGB7_ENST00000422257.3_Silent_p.Q696Q	NM_000889.1	NP_000880.1	P26010	ITB7_HUMAN	integrin, beta 7	696					cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|cell-matrix adhesion involved in ameboidal cell migration (GO:0003366)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte tethering or rolling (GO:0050901)|multicellular organismal development (GO:0007275)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|substrate adhesion-dependent cell spreading (GO:0034446)|T cell migration (GO:0072678)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alpha4-beta7 complex (GO:0034669)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)|virus receptor activity (GO:0001618)			NS(2)|breast(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(3)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						AGAAGAACAGCTGGTTGTCCA	0.567																																						ENST00000267082.5																			0				NS(2)|breast(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(3)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						c.(2086-2088)caG>caA		integrin, beta 7							140.0	125.0	130.0					12																	53586181		2203	4300	6503	SO:0001819	synonymous_variant	3695				cell-matrix adhesion|integrin-mediated signaling pathway|multicellular organismal development|regulation of immune response	integrin complex	identical protein binding|metal ion binding|receptor activity	g.chr12:53586181C>T		CCDS8849.1	12q13.1	2010-03-23				ENSG00000139626		"""Integrins"""	6162	protein-coding gene	gene with protein product		147559				2040616	Standard	XM_005268851		Approved		uc001scc.3	P26010		ENST00000267082.5:c.2088G>A	12.37:g.53586181C>T						ITGB7_ENST00000422257.3_Silent_p.Q696Q|ITGB7_ENST00000338737.4_Silent_p.Q548Q|ITGB7_ENST00000550743.2_Silent_p.Q548Q	p.Q696Q	NM_000889.1	NP_000880.1	P26010	ITB7_HUMAN			14	2319	-			696					Q9UCP7|Q9UCS7	Silent	SNP	ENST00000267082.5	37	c.2088G>A	CCDS8849.1																																																																																				0.567	ITGB7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405821.2			13	81	0	0	0	1	0	13	81				
ACOT1	641371	broad.mit.edu	37	14	74008372	74008372	+	Silent	SNP	T	T	C	rs371750964	byFrequency	TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	d6d2a21b-6095-4ec9-8254-e5d2564aad50	g.chr14:74008372T>C	ENST00000311148.4	+	2	941	c.633T>C	c.(631-633)gcT>gcC	p.A211A	HEATR4_ENST00000560393.1_Intron|HEATR4_ENST00000334988.2_Intron|ACOT1_ENST00000557556.1_Silent_p.A211A|HEATR4_ENST00000553558.1_Intron	NM_001037161.1	NP_001032238.1	Q86TX2	ACOT1_HUMAN	acyl-CoA thioesterase 1	211					acyl-CoA metabolic process (GO:0006637)|long-chain fatty acid metabolic process (GO:0001676)|very long-chain fatty acid metabolic process (GO:0000038)	cytosol (GO:0005829)	acyl-CoA hydrolase activity (GO:0047617)|carboxylic ester hydrolase activity (GO:0052689)|palmitoyl-CoA hydrolase activity (GO:0016290)			endometrium(1)|large_intestine(1)|lung(2)	4				OV - Ovarian serous cystadenocarcinoma(108;1.37e-45)|BRCA - Breast invasive adenocarcinoma(234;0.0033)		TTGAAGAAGCTGTGAACTACT	0.458													-|||	65	0.0129792	0.0257	0.0115	5008	,	,		10110	0.002		0.0139	False		,,,				2504	0.0072					ENST00000311148.4																			0				endometrium(1)|large_intestine(1)|lung(2)	4						c.(631-633)gcT>gcC		acyl-CoA thioesterase 1																																				SO:0001819	synonymous_variant	641371							g.chr14:74008372T>C	DQ082754	CCDS32117.1	14q24.3	2013-09-20			ENSG00000184227	ENSG00000184227		"""Acyl CoA thioesterases"""	33128	protein-coding gene	gene with protein product		614313				16103133, 16940157	Standard	NM_001037161		Approved	ACH2, CTE-1, LACH2		Q86TX2	OTTHUMG00000171607	ENST00000311148.4:c.633T>C	14.37:g.74008372T>C						ACOT1_ENST00000557556.1_Silent_p.A211A|HEATR4_ENST00000553558.1_Intron|HEATR4_ENST00000334988.2_Intron|HEATR4_ENST00000560393.1_Intron	p.A211A	NM_001037161.1	NP_001032238.1				OV - Ovarian serous cystadenocarcinoma(108;1.37e-45)|BRCA - Breast invasive adenocarcinoma(234;0.0033)	2	941	+								A1L173|Q3I5F9	Silent	SNP	ENST00000311148.4	37	c.633T>C	CCDS32117.1																																																																																				0.458	ACOT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414432.1	NM_001037161		4	47	0	0	0	1	0	4	47				
PRG4	10216	broad.mit.edu	37	1	186276143	186276145	+	In_Frame_Del	DEL	CTC	CTC	-			TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	c181d15b-c8ae-4d11-b57f-8de22eb27f81	g.chr1:186276143_186276145delCTC	ENST00000445192.2	+	7	1337_1339	c.1292_1294delCTC	c.(1291-1296)actccc>acc	p.P432del	PRG4_ENST00000367484.3_Intron|PRG4_ENST00000367486.3_In_Frame_Del_p.P389del|PRG4_ENST00000367483.4_In_Frame_Del_p.P391del|PRG4_ENST00000367485.4_In_Frame_Del_p.P339del	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	432	59 X 8 AA repeats of K-X-P-X-P-T-T-X.				cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						GCACCCACCACTCCCAAGGAGCC	0.655																																						ENST00000445192.2																			0				NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						c.(1291-1296)acc>a		proteoglycan 4																																				SO:0001651	inframe_deletion	10216				cell proliferation|immune response	extracellular region	polysaccharide binding|protein binding|scavenger receptor activity	g.chr1:186276143_186276145delCTC	U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"""lubricin"", ""megakaryocyte stimulating factor"", ""articular superficial zone protein"", ""Jacobs camptodactyly-arthropathy-pericarditis syndrome"", ""camptodactyly, arthropathy, coxa vara, pericarditis syndrome"", ""bG174L6.2 (MSF: megakaryocyte stimulating factor )"""	604283	"""proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"""	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.1292_1294delCTC	1.37:g.186276143_186276145delCTC	ENSP00000399679:p.Pro432del					PRG4_ENST00000367485.4_In_Frame_Del_p.TP338del|PRG4_ENST00000367484.3_Intron|PRG4_ENST00000367483.4_In_Frame_Del_p.TP390del|PRG4_ENST00000367486.3_In_Frame_Del_p.TP388del	p.TP431del	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN			7	1337_1339	+			431			59 X 8 AA repeats of K-X-P-X-P-T-T-X.		Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	In_Frame_Del	DEL	ENST00000445192.2	37	c.1292_1294delCTC	CCDS1369.1																																																																																				0.655	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807		10	109						10	109	---	---	---	---
TMCC1	23023	broad.mit.edu	37	3	129370576	129370578	+	In_Frame_Del	DEL	CTG	CTG	-			TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	c181d15b-c8ae-4d11-b57f-8de22eb27f81	g.chr3:129370576_129370578delCTG	ENST00000393238.3	-	6	2048_2050	c.1708_1710delCAG	c.(1708-1710)cagdel	p.Q570del	TMCC1_ENST00000432054.2_In_Frame_Del_p.Q246del|TMCC1_ENST00000426664.2_In_Frame_Del_p.Q456del|TMCC1_ENST00000329333.5_In_Frame_Del_p.Q391del	NM_001017395.3	NP_001017395.2	O94876	TMCC1_HUMAN	transmembrane and coiled-coil domain family 1	570						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)			PLXND1/TMCC1(4)	breast(1)|endometrium(3)|large_intestine(8)|lung(12)|skin(1)	25						GCTGCACCACCTGCTGCTGCTGC	0.581																																						ENST00000393238.3																		PLXND1/TMCC1(4)	0				breast(1)|endometrium(3)|large_intestine(8)|lung(12)|skin(1)	25						c.(1708-1710)del		transmembrane and coiled-coil domain family 1																																				SO:0001651	inframe_deletion	23023					integral to membrane		g.chr3:129370576_129370578delCTG	AB018322	CCDS33855.1	3q21.3	2010-04-19	2005-07-13		ENSG00000172765	ENSG00000172765		"""Transmembrane and coiled-coil domain containing"""	29116	protein-coding gene	gene with protein product			"""transmembrane and coiled-coil domains 1"""			9872452	Standard	NR_033361		Approved	KIAA0779	uc021xdy.1	O94876	OTTHUMG00000159579	ENST00000393238.3:c.1708_1710delCAG	3.37:g.129370585_129370587delCTG	ENSP00000376930:p.Gln570del					TMCC1_ENST00000329333.5_In_Frame_Del_p.Q391del|TMCC1_ENST00000426664.2_In_Frame_Del_p.Q456del|TMCC1_ENST00000432054.2_In_Frame_Del_p.Q246del	p.Q570del	NM_001017395.3	NP_001017395.2	O94876	TMCC1_HUMAN			6	2048_2050	-			570					A8K5Y3|B4DE04|Q68E06|Q8IXM8	In_Frame_Del	DEL	ENST00000393238.3	37	c.1708_1710delCAG	CCDS33855.1																																																																																				0.581	TMCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356418.2	NM_015008		7	80						7	80	---	---	---	---
PMS2P4	5382	broad.mit.edu	37	7	66762433	66762433	+	RNA	DEL	A	A	-	rs530279026	byFrequency	TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	c181d15b-c8ae-4d11-b57f-8de22eb27f81	g.chr7:66762433delA	ENST00000414507.1	-	0	184				Y_RNA_ENST00000364695.1_RNA					postmeiotic segregation increased 2 pseudogene 4																		tctcaaaaagaaaaaaaaaaa	0.408													|||unknown(HR)	2771	0.553315	0.6127	0.5648	5008	,	,		17205	0.5159		0.5129	False		,,,				2504	0.545					ENST00000414507.1																			0																																																			0							g.chr7:66762433delA	D38438		7q11.22	2010-10-26	2010-10-26	2010-10-26	ENSG00000067601	ENSG00000067601			9129	pseudogene	pseudogene	"""PMS2 pseudogene"""		"""postmeiotic segregation increased 2-like 4"", ""postmeiotic segregation increased 2-like 4 pseudogene"""	PMS2L4		8586419	Standard	NR_046297		Approved	PMS6	uc003tvo.3		OTTHUMG00000156923		7.37:g.66762433delA														0	184	-									RNA	DEL	ENST00000414507.1	37																																																																																						0.408	PMS2P4-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000346632.1	NR_022007		7	8						7	8	---	---	---	---
NUFIP2	57532	broad.mit.edu	37	17	27620990	27620992	+	In_Frame_Del	DEL	GCT	GCT	-			TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	c181d15b-c8ae-4d11-b57f-8de22eb27f81	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		7	101						7	101	---	---	---	---
IGLC3	3539	broad.mit.edu	37	22	23248852	23248852	+	RNA	DEL	A	A	-	rs71797740|rs200606818	byFrequency	TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	c181d15b-c8ae-4d11-b57f-8de22eb27f81	g.chr22:23248852delA	ENST00000390325.2	+	0	341				IGLJ3_ENST00000390324.2_RNA			P0CG06	LAC3_HUMAN	immunoglobulin lambda constant 3 (Kern-Oz+ marker)						complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|regulation of immune response (GO:0050776)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)										CTCACCCCCCACCACGGGAGA	0.572													-|A|-|insertion	1080	0.215655	0.1271	0.2565	5008	,	,		20361	0.3879		0.0974	False		,,,				2504	0.2505					ENST00000390325.2																			0																	813,2575		63,687,944						-2.4	0.0		dbSNP_130	7	1378,5566		50,1278,2144	no	intergenic				113,1965,3088	A1A1,A1R,RR		19.8445,23.9965,21.206				2191,8141						0							g.chr22:23248852delA	J00254		22q11.2	2012-02-08			ENSG00000211679	ENSG00000211679		"""Immunoglobulins / IGL locus"""	5857	other	immunoglobulin gene				IGLC			Standard	NG_000002		Approved			P0CG06	OTTHUMG00000151217		22.37:g.23248852delA														0	341	+								A0M8Q4|P80423	RNA	DEL	ENST00000390325.2	37																																																																																						0.572	IGLC3-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal	IG_C_gene	IG_C_gene	OTTHUMT00000321821.3	NG_000002		9	35						9	35	---	---	---	---
DND1	373863	broad.mit.edu	37	5	140052285	140052285	+	Frame_Shift_Del	DEL	T	T	-	rs375722663	byFrequency	TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	d6d2a21b-6095-4ec9-8254-e5d2564aad50	g.chr5:140052285delT	ENST00000542735.1	-	3	392	c.349delA	c.(349-351)acgfs	p.T117fs		NM_194249.2	NP_919225.1	Q8IYX4	DND1_HUMAN	DND microRNA-mediated repression inhibitor 1	117	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|negative regulation of gene silencing by miRNA (GO:0060965)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|nucleotide binding (GO:0000166)	p.T117fs*24(1)		central_nervous_system(1)|prostate(4)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTGTGCAGCGTGGCGATGGCG	0.682													T|T|-|deletion	29	0.00579073	0.0	0.0173	5008	,	,		10844	0.002		0.0139	False		,,,				2504	0.001					ENST00000542735.1																			1	Deletion - Frameshift(1)	p.T117fs*24(1)	central_nervous_system(1)	central_nervous_system(1)|prostate(4)	5						c.(349-351)cgfs		DND microRNA-mediated repression inhibitor 1							6.0	7.0	6.0					5																	140052285		2084	4099	6183	SO:0001589	frameshift_variant	373863				multicellular organismal development|negative regulation of gene silencing by miRNA	cytoplasm|nucleus	AU-rich element binding|nucleotide binding	g.chr5:140052285delT	AY321065	CCDS4236.1	5q31.3	2013-07-31	2013-07-31		ENSG00000256453	ENSG00000256453		"""RNA binding motif (RRM) containing"""	23799	protein-coding gene	gene with protein product		609385	"""dead end homolog 1 (zebrafish)"""			12932328	Standard	NM_194249		Approved	MGC34750, RBMS4	uc003lgt.3	Q8IYX4	OTTHUMG00000129499	ENST00000542735.1:c.349delA	5.37:g.140052285delT	ENSP00000445366:p.Thr117fs						p.T117fs	NM_194249.2	NP_919225.1	Q8IYX4	DND1_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		3	392	-			117			RRM 1.			Frame_Shift_Del	DEL	ENST00000542735.1	37	c.349delA	CCDS4236.1																																																																																				0.682	DND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251669.2	NM_194249		10	28						10	28	---	---	---	---
