#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
GOLGA6L3	100133220	broad.mit.edu	37	15	83014132	83014132	+	Missense_Mutation	SNP	C	C	G			TCGA-06-0178-01A-01D-1491-08	TCGA-06-0178-10B-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4fa779b-d116-4696-b170-60f3e215e9fb	c9f63961-b124-468a-bff1-62c1aedd1805	g.chr15:83014132C>G	ENST00000557886.1	-	6	550	c.451G>C	c.(451-453)Gag>Cag	p.E151Q															p.E151Q(4)		endometrium(6)|kidney(5)|prostate(1)	12						GCTGGGGGCTCTGGGGCCAGG	0.522																																						uc021ssz.1																			4	Substitution - Missense(4)	p.E151Q(4)	kidney(4)	endometrium(1)|kidney(4)	5						c.(415-417)Gag>Cag		Homo sapiens golgin A6 family-like 10 (GOLGA6L10), mRNA.																																				SO:0001583	missense	647042							g.chr15:83014132C>G																												ENST00000557886.1:c.451G>C	15.37:g.83014132C>G	ENSP00000452844:p.Glu151Gln					LOC440295_uc002bhl.2_Intron|GOLGA6L9_uc021ssr.1_Intron|LOC440295_uc002bhm.2_Intron|GOLGA6L10_uc021sta.1_Non-coding_Transcript	p.E139Q			A6NI86	GG6LA_HUMAN			5	551	-			151						Missense_Mutation	SNP	ENST00000557886.1	37	c.415G>C																																																																																					0.522	RP13-996F3.4-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000419277.1		
MYO1D	4642	broad.mit.edu	37	17	31203857	31203857	+	Frame_Shift_Del	DEL	C	C	-			TCGA-06-0178-01A-01D-1491-08	TCGA-06-0178-10B-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4fa779b-d116-4696-b170-60f3e215e9fb	c9f63961-b124-468a-bff1-62c1aedd1805	g.chr17:31203857delC	ENST00000318217.5	-	1	338	c.34delG	c.(34-36)gcafs	p.A12fs	AC084809.2_ENST00000435733.1_RNA|MYO1D_ENST00000579584.1_Frame_Shift_Del_p.A12fs|MYO1D_ENST00000583621.1_Frame_Shift_Del_p.A12fs	NM_015194.1	NP_056009.1	O94832	MYO1D_HUMAN	myosin ID	12	Myosin motor.				early endosome to recycling endosome transport (GO:0061502)|negative regulation of phosphatase activity (GO:0010923)	axolemma (GO:0030673)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|smooth endoplasmic reticulum (GO:0005790)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(14)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39			BRCA - Breast invasive adenocarcinoma(9;0.0362)			ACGAAGTCTGCCTTGCCGAAT	0.726																																						uc002hho.1																			0				breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(14)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						c.(34-36)gcafs		Homo sapiens myosin ID (MYO1D), mRNA.							30.0	21.0	24.0					17																	31203857		2181	4273	6454	SO:0001589	frameshift_variant	4642					myosin complex	actin binding|ATP binding|calmodulin binding	g.chr17:31203857delC	AB018270	CCDS32615.1	17q11-q12	2014-06-12				ENSG00000176658		"""Myosins / Myosin superfamily : Class I"""	7598	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 108"""	606539				8884266	Standard	NM_015194		Approved	KIAA0727, myr4, PPP1R108	uc002hho.1	O94832		ENST00000318217.5:c.34delG	17.37:g.31203857delC	ENSP00000324527:p.Ala12fs					MYO1D_uc002hhp.1_Frame_Shift_Del_p.A12fs|MYO1D_uc010wcb.2_Frame_Shift_Del_p.A12fs	p.A12fs	NM_015194	NP_056009	O94832	MYO1D_HUMAN	BRCA - Breast invasive adenocarcinoma(9;0.0362)		0	46	-			12			Myosin head-like.		A6H8V3|Q8NHP9	Frame_Shift_Del	DEL	ENST00000318217.5	37	c.34delG	CCDS32615.1																																																																																				0.726	MYO1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447457.1		
SYNE1	23345	broad.mit.edu	37	6	152665261	152665261	+	Missense_Mutation	SNP	C	C	A	rs4645434	byFrequency	TCGA-06-0178-01A-01D-1491-08	TCGA-06-0178-10B-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4fa779b-d116-4696-b170-60f3e215e9fb	c9f63961-b124-468a-bff1-62c1aedd1805	g.chr6:152665261C>A	ENST00000367255.5	-	74	12781	c.12180G>T	c.(12178-12180)gaG>gaT	p.E4060D	SYNE1_ENST00000265368.4_Missense_Mutation_p.E4060D|SYNE1_ENST00000341594.5_Missense_Mutation_p.E3925D|SYNE1_ENST00000448038.1_Missense_Mutation_p.E3989D|SYNE1_ENST00000423061.1_Missense_Mutation_p.E3989D	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	4060			E -> D (in dbSNP:rs4645434).		cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.E4060D(3)		NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		GAGGACTTGGCTCTAAATCCG	0.498										HNSCC(10;0.0054)			C|||	2732	0.545527	0.4138	0.6182	5008	,	,		18310	0.6488		0.6024	False		,,,				2504	0.5072					uc021zhb.1																			3	Substitution - Missense(3)	p.E4060D(5)	skin(2)|central_nervous_system(1)	NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524						c.(12178-12180)gaG>gaT		Homo sapiens spectrin repeat containing, nuclear envelope 1 (SYNE1), transcript variant 1, mRNA.		C	ASP/GLU,ASP/GLU	2065,2341	569.8+/-382.7	487,1091,625	106.0	102.0	103.0		11967,12180	-1.2	0.0	6	dbSNP_111	103	5313,3287	647.1+/-400.3	1664,1985,651	yes	missense,missense	SYNE1	NM_033071.3,NM_182961.3	45,45	2151,3076,1276	AA,AC,CC		38.2209,46.8679,43.2723	benign,benign	3989/8750,4060/8798	152665261	7378,5628	2203	4300	6503	SO:0001583	missense	23345				cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding	g.chr6:152665261C>A	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"""myocyte nuclear envelope protein 1"", ""nuclear envelope spectrin repeat-1"""	608441	"""chromosome 6 open reading frame 98"""	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.12180G>T	6.37:g.152665261C>A	ENSP00000356224:p.Glu4060Asp	HNSCC(10;0.0054)				SYNE1_uc003qot.4_Missense_Mutation_p.E3989D|SYNE1_uc003qou.4_Missense_Mutation_p.E4060D|SYNE1_uc010kja.2_Missense_Mutation_p.E765D	p.E4060D	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)	71	12403	-		Ovarian(120;0.0955)	4060		E -> D (in dbSNP:rs4645434).			E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	c.12180G>T	CCDS5236.2	1271	0.581959706959707	217	0.4410569105691057	222	0.6132596685082873	373	0.6520979020979021	459	0.6055408970976254	C	6.405	0.442830	0.12164	0.468679	0.617791	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	T;T;T;T;T	0.35048	1.33;1.33;1.33;1.33;1.33	5.76	-1.25	0.09405	.	0.176957	0.39341	N	0.001392	T	0.05914	0.0154	N	0.14661	0.345	0.22911	P	0.99857779	B;B;B;B	0.28208	0.203;0.203;0.203;0.082	B;B;B;B	0.24541	0.031;0.031;0.031;0.054	T	0.36187	-0.9758	9	0.11182	T	0.66	.	10.9634	0.47397	0.0:0.4861:0.0:0.5139	rs4645434;rs52832929;rs56482475;rs57199459;rs4645434	4060;4060;4060;3989	B7ZBC3;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	D	4060;3989;4060;3989;3925	ENSP00000356224:E4060D;ENSP00000396024:E3989D;ENSP00000265368:E4060D;ENSP00000390975:E3989D;ENSP00000341887:E3925D	ENSP00000265368:E4060D	E	-	3	2	SYNE1	152706954	0.996000	0.38824	0.016000	0.15963	0.190000	0.23558	0.426000	0.21363	-0.234000	0.09782	-0.749000	0.03505	GAG		0.498	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
LPAL2	80350	broad.mit.edu	37	6	160898160	160898160	+	RNA	SNP	C	C	T	rs2048328	byFrequency	TCGA-06-0178-01A-01D-1491-08	TCGA-06-0178-10B-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4fa779b-d116-4696-b170-60f3e215e9fb	c9f63961-b124-468a-bff1-62c1aedd1805	g.chr6:160898160C>T	ENST00000335388.5	-	0	1505					NR_028092.1		Q16609	LPAL2_HUMAN	lipoprotein, Lp(a)-like 2, pseudogene							extracellular region (GO:0005576)				large_intestine(1)|lung(4)	5		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.214)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)		CAAAGACATACTCATTTGGGT	0.453													C|||	1029	0.205471	0.0628	0.1772	5008	,	,		20633	0.3492		0.1998	False		,,,				2504	0.2761					uc003qtj.2																			0				large_intestine(1)|lung(4)	5						c.e9+1		Homo sapiens lipoprotein, Lp(a)-like 2, pseudogene (LPAL2), transcript variant 2, non-coding RNA.																																						80350							g.chr6:160898160C>T	U19517		6q26-q27	2010-10-27	2010-10-27	2004-02-18	ENSG00000213071	ENSG00000213071			21210	pseudogene	pseudogene		611682	"""apolipoprotein A-like"", ""lipoprotein, Lp(a)-like 2"""	APOAL		7749817, 7679504	Standard	NR_028092		Approved	APOARGC	uc011efy.2	Q16609	OTTHUMG00000015952		6.37:g.160898160C>T						LPAL2_uc011efy.2_Splice_Site							OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	9		-		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.214)						E1P5B4	Splice_Site	SNP	ENST00000335388.5	37	c.1505_splice																																																																																					0.453	LPAL2-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000042950.1	NM_024492	
SFT2D1	113402	broad.mit.edu	37	6	166739646	166739646	+	Missense_Mutation	SNP	T	T	C	rs11551053	byFrequency	TCGA-06-0178-01A-01D-1491-08	TCGA-06-0178-10B-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4fa779b-d116-4696-b170-60f3e215e9fb	c9f63961-b124-468a-bff1-62c1aedd1805	g.chr6:166739646T>C	ENST00000361731.3	-	5	434	c.325A>G	c.(325-327)Ata>Gta	p.I109V	SFT2D1_ENST00000487841.1_5'UTR	NM_145169.1	NP_660152.1			SFT2 domain containing 1									p.I109V(1)		NS(1)|central_nervous_system(1)|large_intestine(3)|upper_aerodigestive_tract(1)	6		Breast(66;0.000148)|Prostate(117;0.109)|Ovarian(120;0.199)		OV - Ovarian serous cystadenocarcinoma(33;2.63e-19)|BRCA - Breast invasive adenocarcinoma(81;4.92e-06)|GBM - Glioblastoma multiforme(31;4.58e-05)		AGGGTAAATATGAAACACAAC	0.413													C|||	557	0.111222	0.0356	0.0793	5008	,	,		18011	0.3313		0.0398	False		,,,				2504	0.0828					uc003qux.3																			1	Substitution - Missense(1)	p.I109V(2)	central_nervous_system(1)	NS(1)|central_nervous_system(1)|large_intestine(3)|upper_aerodigestive_tract(1)	6						c.(325-327)Ata>Gta		Homo sapiens SFT2 domain containing 1 (SFT2D1), mRNA.		C	VAL/ILE	147,4259	812.6+/-416.1	1,145,2057	82.0	78.0	79.0		325	-1.3	0.0	6	dbSNP_120	79	304,8296	805.6+/-407.3	5,294,4001	yes	missense	SFT2D1	NM_145169.1	29	6,439,6058	CC,CT,TT		3.5349,3.3364,3.4676	benign	109/160	166739646	451,12555	2203	4300	6503	SO:0001583	missense	113402				protein transport|vesicle-mediated transport	integral to membrane		g.chr6:166739646T>C	AF041429	CCDS5292.1	6q27	2008-02-05	2005-07-25	2005-07-25	ENSG00000198818	ENSG00000198818			21102	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 83"""	C6orf83			Standard	NM_145169		Approved	MGC19825, pRGR1	uc003qux.3	Q8WV19	OTTHUMG00000016001	ENST00000361731.3:c.325A>G	6.37:g.166739646T>C	ENSP00000354590:p.Ile109Val						p.I109V	NM_145169	NP_660152	Q8WV19	SFT2A_HUMAN		OV - Ovarian serous cystadenocarcinoma(33;2.63e-19)|BRCA - Breast invasive adenocarcinoma(81;4.92e-06)|GBM - Glioblastoma multiforme(31;4.58e-05)	4	347	-		Breast(66;0.000148)|Prostate(117;0.109)|Ovarian(120;0.199)	109		I -> V (in dbSNP:rs11551053).				Missense_Mutation	SNP	ENST00000361731.3	37	c.325A>G	CCDS5292.1	278	0.12728937728937728	19	0.03861788617886179	26	0.0718232044198895	199	0.3479020979020979	34	0.044854881266490766	C	0	-2.803354	0.00075	0.033364	0.035349	ENSG00000198818	ENST00000361731	T	0.58652	0.32	4.98	-1.34	0.09143	.	0.690574	0.13904	N	0.354704	T	0.07458	0.0188	N	0.03209	-0.39	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.25012	-1.0144	9	0.02654	T	1	-6.1183	5.4909	0.16774	0.1304:0.4651:0.0:0.4045	rs11551053;rs36102427;rs60635309	109	Q8WV19	SFT2A_HUMAN	V	109	ENSP00000354590:I109V	ENSP00000354590:I109V	I	-	1	0	SFT2D1	166659636	0.000000	0.05858	0.001000	0.08648	0.007000	0.05969	-1.557000	0.02166	-0.259000	0.09432	-1.008000	0.02478	ATA		0.413	SFT2D1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043061.2	NM_145169	
