bio-locus 0.0.2

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Files changed (24) hide show
  1. checksums.yaml +7 -0
  2. data/.document +5 -0
  3. data/.rspec +1 -0
  4. data/.travis.yml +13 -0
  5. data/Gemfile +14 -0
  6. data/LICENSE.txt +20 -0
  7. data/README.md +162 -0
  8. data/Rakefile +52 -0
  9. data/VERSION +1 -0
  10. data/bin/bio-locus +117 -0
  11. data/features/bio-locus.feature +9 -0
  12. data/features/step_definitions/bio-locus_steps.rb +0 -0
  13. data/features/support/env.rb +13 -0
  14. data/lib/bio-locus.rb +12 -0
  15. data/lib/bio-locus/locus.rb +49 -0
  16. data/lib/bio-locus/match.rb +43 -0
  17. data/lib/bio-locus/store.rb +29 -0
  18. data/spec/bio-locus_spec.rb +7 -0
  19. data/spec/spec_helper.rb +12 -0
  20. data/test/data/input/dbsnp.vcf +200 -0
  21. data/test/data/input/multisample.vcf +150 -0
  22. data/test/data/input/somaticsniper.vcf +87 -0
  23. data/test/data/input/test.snv1 +106 -0
  24. metadata +139 -0
data/test/data/input/somaticsniper.vcf ADDED
@@ -0,0 +1,87 @@
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+ ##fileformat=VCFv4.1
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+ ##fileDate=20140121
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+ ##phasing=none
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+ ##reference=file:///data/GENOMES/human_GATK_GRCh37/GRCh37_gatk.fasta
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+ ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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+ ##FORMAT=<ID=IGT,Number=1,Type=String,Description="Genotype when called independently (only filled if called in joint prior mode)">
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+ ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Total read depth">
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+ ##FORMAT=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
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+ ##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description="Occurrence count for each base at this site (A,C,G,T)">
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+ ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality">
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+ ##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description="Joint genotype quality (only filled if called in join prior mode)">
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+ ##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description="Variant allele quality">
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+ ##FORMAT=<ID=BQ,Number=.,Type=Integer,Description="Average base quality">
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+ ##FORMAT=<ID=MQ,Number=1,Type=Integer,Description="Average mapping quality across all reads">
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+ ##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description="Average mapping quality for each allele present in the genotype">
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+ ##FORMAT=<ID=SS,Number=1,Type=Integer,Description="Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown">
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+ ##FORMAT=<ID=SSC,Number=1,Type=Integer,Description="Somatic Score">
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+ #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR
19
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+ 15 43170722 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:11:6,5,0,0:0,11,0,0:60:31:0:60:37:37:0:. 0/1:0/1:6:4,0,2,0:0,4,0,2:24:31:24:56,54:37:37,37:2:31
71
+ 15 50862183 . C A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:9:7,2,0,0:0,9,0,0:54:35:0:60:37:37:0:. 0/1:0/1:4:0,2,0,2:2,2,0,0:28:35:28:45,59:37:37,37:2:33
72
+ 15 64332347 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:7:6,1,0,0:0,7,0,0:48:39:0:60:37:37:0:. 0/1:0/1:5:3,0,1,1:0,3,0,2:32:39:32:58,56:37:37,37:2:30
73
+ 15 80845030 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:9:1,8,0,0:0,9,0,0:54:31:0:60:37:37:0:. 0/1:0/1:6:2,2,2,0:0,4,0,2:24:31:24:60,60:37:37,37:2:30
74
+ 16 1812938 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:11:8,3,0,0:0,0,11,0:60:34:0:46:37:37:0:. 0/1:0/1:5:1,2,1,1:2,0,3,0:27:34:27:46,55:37:37,37:2:33
75
+ 16 3582808 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:10:6,4,0,0:0,0,10,0:57:34:0:59:37:37:0:. 0/1:0/1:5:0,3,2,0:2,0,3,0:27:34:27:60,60:37:37,37:2:33
76
+ 16 14042032 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:7:6,1,0,0:0,7,0,0:48:37:0:60:37:37:0:. 0/1:0/1:4:0,2,2,0:0,2,0,2:30:37:30:57,60:37:37,37:2:30
77
+ 16 23619204 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:7:5,2,0,0:0,0,7,0:48:42:0:60:37:37:0:. 0/1:0/1:4:1,1,1,1:2,0,2,0:35:42:35:60,60:37:37,37:2:31
78
+ 17 41256142 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:8:5,3,0,0:0,0,8,0:51:40:0:60:37:37:0:. 0/1:0/1:3:0,1,2,0:2,0,1,0:1:40:33:57,60:37:37,37:2:33
79
+ 17 61784013 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:9:6,3,0,0:0,9,0,0:54:45:0:60:37:37:0:. 0/1:0/1:3:0,1,1,1:0,1,0,2:1:45:34:60,60:37:37,37:2:36
80
+ 18 45423074 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:16:8,8,0,0:0,16,0,0:75:46:0:53:37:37:0:. 0/1:0/1:10:3,4,3,0:0,7,0,3:39:46:39:60,60:37:37,37:2:46
81
+ 18 60985432 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:14:9,4,0,1:0,0,13,0:32:42:0:60:37:37:0:. 0/1:0/1:4:2,0,1,1:2,0,2,0:30:42:35:60,57:37:37,37:2:41
82
+ 19 39664512 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:14:8,6,0,0:0,14,0,0:69:42:0:60:37:37:0:. 0/1:0/1:4:0,2,1,1:0,2,0,2:30:42:35:60,60:37:37,37:2:42
83
+ 19 49473085 . G C . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:8:4,4,0,0:0,0,8,0:51:37:0:60:37:37:0:. 0/1:0/1:4:1,1,2,0:0,2,2,0:30:37:30:48,56:37:37,37:2:32
84
+ 20 34135210 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:8:2,6,0,0:0,8,0,0:51:36:0:59:37:37:0:. 0/1:0/1:6:2,2,1,1:0,4,0,2:29:36:29:60,60:37:37,37:2:32
85
+ 20 35663882 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:7:2,5,0,0:0,0,7,0:48:37:0:56:37:37:0:. 0/1:0/1:4:1,1,0,2:2,0,2,0:30:37:30:60,60:37:37,37:2:30
86
+ X 70341572 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:11:6,5,0,0:0,11,0,0:60:33:0:56:37:37:0:. 0/1:0/1:7:3,2,1,1:0,5,0,2:26:33:26:58,60:37:37,37:2:33
87
+ X 123164862 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:7:5,2,0,0:0,0,7,0:48:40:0:59:37:37:0:. 0/1:0/1:3:1,0,2,0:2,0,1,0:1:40:33:60,60:37:37,37:2:30
data/test/data/input/test.snv1 ADDED
@@ -0,0 +1,106 @@
1
+ ##ANNOTATOR_SETTINGS: SCRIPT_NAME=annotator.pl;SCRIPT_VERSION=11;HOST=wgs10.op.umcutrecht.nl;ENSEMBL_VERSION=72;DBSNP_VERSION=137;GERP_ALIGN_SET=mammals;INPUT_FILE_TYPE:pipelineRefiltered
2
+ #chr pos na_change strand raw_cov inf_cov inf_pnr aa_change genotype gene_name ccds_id codon snp_id effect hgvs_t hgvs_p polyphen_s polyphen_p sift_s sift_p grantham gerp gerp_region high_freq high_popu gene_id tran_id prot_id biotype ncbi36_hg18 info
3
+ 1 223988462 G/A -1 11 0 G L297F A TP53BP2 CCDS1538 Ctt/Ttt novel missense_variant ENST00000391878.2:c.889C>T ENSP00000375750.2:p.Leu297Phe 0.001 benign 0.7 tolerated 22 0.790 1.755 NA NA ENSG00000143514 ENST00000391878 ENSP00000375750 protein_coding 1_222055085 REFSEQ_P=NP_005417 | UNIPROT=Q13625 | REFSEQ_T=NM_005426.2 | GENE_DESC=tumor protein p53 binding protein, 2 [Source:HGNC Symbol;Acc:12000] | MIM_DESC= | UNIGENE=Hs.708253;Hs.523968 | MIM_ID=
4
+ 1 223988462 G/A -1 11 0 G L426F A TP53BP2 CCDS44319 Ctt/Ttt novel missense_variant ENST00000343537.7:c.1276C>T ENSP00000341957.7:p.Leu426Phe 0.001 benign 0.7 tolerated 22 0.790 1.755 NA NA ENSG00000143514 ENST00000343537 ENSP00000341957 protein_coding 1_222055085 REFSEQ_P=NP_001026855 | UNIPROT=Q13625 | REFSEQ_T=NM_001031685.2 | GENE_DESC=tumor protein p53 binding protein, 2 [Source:HGNC Symbol;Acc:12000] | MIM_DESC= | UNIGENE=Hs.708253;Hs.523968 | MIM_ID=
5
+ 1 227504819 T/C -1 8 0 T N22S C CDC42BPA CCDS1558 aAt/aGt novel missense_variant ENST00000366769.3:c.65A>G ENSP00000355731.3:p.Asn22Ser 0.001 benign 0.38 tolerated 46 1.960 2.287 NA NA ENSG00000143776 ENST00000366769 ENSP00000355731 protein_coding 1_225571442 REFSEQ_P=NP_003598 | UNIPROT=Q5VT25 | REFSEQ_T=NM_003607.3 | GENE_DESC=CDC42 binding protein kinase alpha (DMPK-like) [Source:HGNC Symbol;Acc:1737] | MIM_DESC= | UNIGENE=Hs.605778;Hs.35433;Hs.623470;Hs.604610 | MIM_ID=
6
+ 1 227504819 T/C -1 8 0 T N22S C CDC42BPA NA aAt/aGt novel missense_variant ENST00000366765.3:c.65A>G ENSP00000355727.3:p.Asn22Ser 0 benign 0.4 tolerated 46 1.960 2.287 NA NA ENSG00000143776 ENST00000366765 ENSP00000355727 protein_coding 1_225571442 REFSEQ_P= | UNIPROT=Q5VT25 | REFSEQ_T= | GENE_DESC=CDC42 binding protein kinase alpha (DMPK-like) [Source:HGNC Symbol;Acc:1737] | MIM_DESC= | UNIGENE=Hs.605778;Hs.35433;Hs.623470;Hs.604610 | MIM_ID=
7
+ 1 227504819 T/C -1 8 0 T N22S C CDC42BPA NA aAt/aGt novel missense_variant ENST00000366764.2:c.65A>G ENSP00000355726.2:p.Asn22Ser 0.001 benign 0.32 tolerated 46 1.960 2.287 NA NA ENSG00000143776 ENST00000366764 ENSP00000355726 protein_coding 1_225571442 REFSEQ_P= | UNIPROT=Q5VT25 | REFSEQ_T= | GENE_DESC=CDC42 binding protein kinase alpha (DMPK-like) [Source:HGNC Symbol;Acc:1737] | MIM_DESC= | UNIGENE=Hs.605778;Hs.35433;Hs.623470;Hs.604610 | MIM_ID=
8
+ 1 227504819 T/C -1 8 0 T N22S C CDC42BPA NA aAt/aGt novel missense_variant ENST00000334218.5:c.65A>G ENSP00000335341.5:p.Asn22Ser 0.002 benign 0.58 tolerated 46 1.960 2.287 NA NA ENSG00000143776 ENST00000334218 ENSP00000335341 protein_coding 1_225571442 REFSEQ_P= | UNIPROT=Q5VT25 | REFSEQ_T= | GENE_DESC=CDC42 binding protein kinase alpha (DMPK-like) [Source:HGNC Symbol;Acc:1737] | MIM_DESC= | UNIGENE=Hs.605778;Hs.35433;Hs.623470;Hs.604610 | MIM_ID=
9
+ 1 227504819 T/C -1 8 0 T N22S C CDC42BPA CCDS1559 aAt/aGt novel missense_variant ENST00000366767.3:c.65A>G ENSP00000355729.3:p.Asn22Ser 0.003 benign 0.57 tolerated 46 1.960 2.287 NA NA ENSG00000143776 ENST00000366767 ENSP00000355729 protein_coding 1_225571442 REFSEQ_P=NP_055641 | UNIPROT=Q5VT25 | REFSEQ_T=NM_014826.4 | GENE_DESC=CDC42 binding protein kinase alpha (DMPK-like) [Source:HGNC Symbol;Acc:1737] | MIM_DESC= | UNIGENE=Hs.605778;Hs.35433;Hs.623470;Hs.604610 | MIM_ID=
10
+ 1 227504819 T/C -1 8 0 T N22S C CDC42BPA NA aAt/aGt novel missense_variant ENST00000535525.1:c.65A>G ENSP00000443275.1:p.Asn22Ser 0.002 benign 0.54 tolerated 46 1.960 2.287 NA NA ENSG00000143776 ENST00000535525 ENSP00000443275 protein_coding 1_225571442 REFSEQ_P= | UNIPROT= | REFSEQ_T= | GENE_DESC=CDC42 binding protein kinase alpha (DMPK-like) [Source:HGNC Symbol;Acc:1737] | MIM_DESC= | UNIGENE=Hs.605778;Hs.35433;Hs.623470;Hs.604610 | MIM_ID=
11
+ 1 227504819 T/C -1 8 0 T N22S C CDC42BPA NA aAt/aGt novel missense_variant ENST00000366766.2:c.65A>G ENSP00000355728.2:p.Asn22Ser 0.003 benign 0.37 tolerated 46 1.960 2.287 NA NA ENSG00000143776 ENST00000366766 ENSP00000355728 protein_coding 1_225571442 REFSEQ_P= | UNIPROT=Q5VT25 | REFSEQ_T= | GENE_DESC=CDC42 binding protein kinase alpha (DMPK-like) [Source:HGNC Symbol;Acc:1737] | MIM_DESC= | UNIGENE=Hs.605778;Hs.35433;Hs.623470;Hs.604610 | MIM_ID=
12
+ 2 27656583 C/A 1 9 0 C A85D A NRBP1 CCDS1753 gCc/gAc novel missense_variant ENST00000233557.3:c.254C>A ENSP00000233557.3:p.Ala85Asp 0.999 probably damaging 0 deleterious 126 4.000 3.426 NA NA ENSG00000115216 ENST00000233557 ENSP00000233557 protein_coding 2_27510087 REFSEQ_P= | UNIPROT=Q9UHY1 | REFSEQ_T= | GENE_DESC=nuclear receptor binding protein 1 [Source:HGNC Symbol;Acc:7993] | MIM_DESC= | UNIGENE=Hs.739278;Hs.515876;Hs.738928 | MIM_ID=
13
+ 2 27656583 C/A 1 9 0 C A85D A NRBP1 NA gCc/gAc novel missense_variant ENST00000419281.2:c.254C>A ENSP00000403916.2:p.Ala85Asp 0.999 probably damaging 0 deleterious 126 4.000 3.426 NA NA ENSG00000115216 ENST00000419281 ENSP00000403916 protein_coding 2_27510087 REFSEQ_P= | UNIPROT= | REFSEQ_T= | GENE_DESC=nuclear receptor binding protein 1 [Source:HGNC Symbol;Acc:7993] | MIM_DESC= | UNIGENE=Hs.739278;Hs.515876;Hs.738928 | MIM_ID=
14
+ 2 27656583 C/A 1 9 0 C A85D A NRBP1 NA gCc/gAc novel missense_variant ENST00000379863.3:c.254C>A ENSP00000369192.3:p.Ala85Asp 0.999 probably damaging 0 deleterious 126 4.000 3.426 NA NA ENSG00000115216 ENST00000379863 ENSP00000369192 protein_coding 2_27510087 REFSEQ_P= | UNIPROT= | REFSEQ_T= | GENE_DESC=nuclear receptor binding protein 1 [Source:HGNC Symbol;Acc:7993] | MIM_DESC= | UNIGENE=Hs.739278;Hs.515876;Hs.738928 | MIM_ID=
15
+ 2 27656583 C/A 1 9 0 C A85D A NRBP1 CCDS1753 gCc/gAc novel missense_variant ENST00000379852.3:c.254C>A ENSP00000369181.3:p.Ala85Asp 0.999 probably damaging 0 deleterious 126 4.000 3.426 NA NA ENSG00000115216 ENST00000379852 ENSP00000369181 protein_coding 2_27510087 REFSEQ_P=NP_037524 | UNIPROT=Q9UHY1 | REFSEQ_T=NM_013392.2 | GENE_DESC=nuclear receptor binding protein 1 [Source:HGNC Symbol;Acc:7993] | MIM_DESC= | UNIGENE=Hs.739278;Hs.515876;Hs.738928 | MIM_ID=
16
+ 2 102488127 G/C 1 10 0 G D866H C MAP4K4 NA Gac/Cac novel missense_variant ENST00000425019.1:c.2596G>C ENSP00000392830.1:p.Asp866His 0.858 possibly damaging 0.25 tolerated 81 3.730 3.730 NA NA ENSG00000071054 ENST00000425019 ENSP00000392830 protein_coding 2_101854559 REFSEQ_P=NP_663719 | UNIPROT= | REFSEQ_T=NM_145686.3 | GENE_DESC=mitogen-activated protein kinase kinase kinase kinase 4 [Source:HGNC Symbol;Acc:6866] | MIM_DESC= | UNIGENE=Hs.745197 | MIM_ID=
17
+ 2 102488127 G/C 1 10 0 G D873H C MAP4K4 NA Gac/Cac novel missense_variant ENST00000350878.4:c.2617G>C ENSP00000343658.4:p.Asp873His 0 unknown 0.26 tolerated 81 3.730 3.730 NA NA ENSG00000071054 ENST00000350878 ENSP00000343658 protein_coding 2_101854559 REFSEQ_P= | UNIPROT= | REFSEQ_T= | GENE_DESC=mitogen-activated protein kinase kinase kinase kinase 4 [Source:HGNC Symbol;Acc:6866] | MIM_DESC= | UNIGENE=Hs.745197 | MIM_ID=
18
+ 2 201724914 T/C -1 14 0 T R139G C CLK1 CCDS2331 Agg/Ggg novel missense_variant ENST00000321356.4:c.415A>G ENSP00000326830.4:p.Arg139Gly 0.922 probably damaging 0.03 deleterious 125 4.120 3.413 NA NA ENSG00000013441 ENST00000321356 ENSP00000326830 protein_coding 2_201433159 REFSEQ_P=NP_004062 | UNIPROT=P49759 | REFSEQ_T=NM_004071.3 | GENE_DESC=CDC-like kinase 1 [Source:HGNC Symbol;Acc:2068] | MIM_DESC= | UNIGENE=Hs.624435;Hs.433732 | MIM_ID=
19
+ 2 201724914 T/C -1 14 0 T R139G C CLK1 NA Agg/Ggg novel missense_variant ENST00000409403.2:c.415A>G ENSP00000386875.2:p.Arg139Gly 0.998 probably damaging 0.03 deleterious 125 4.120 3.413 NA NA ENSG00000013441 ENST00000409403 ENSP00000386875 protein_coding 2_201433159 REFSEQ_P= | UNIPROT= | REFSEQ_T= | GENE_DESC=CDC-like kinase 1 [Source:HGNC Symbol;Acc:2068] | MIM_DESC= | UNIGENE=Hs.624435;Hs.433732 | MIM_ID=
20
+ 2 201724914 T/C -1 14 0 T R181G C CLK1 CCDS54427 Agg/Ggg novel missense_variant ENST00000434813.2:c.541A>G ENSP00000394734.2:p.Arg181Gly 0.996 probably damaging 0.01 deleterious 125 4.120 3.413 NA NA ENSG00000013441 ENST00000434813 ENSP00000394734 protein_coding 2_201433159 REFSEQ_P=NP_001155879 | UNIPROT=P49759 | REFSEQ_T=NM_001162407.1 | GENE_DESC=CDC-like kinase 1 [Source:HGNC Symbol;Acc:2068] | MIM_DESC= | UNIGENE=Hs.624435;Hs.433732 | MIM_ID=
21
+ 3 178947818 C/T 1 9 0 C T898I T PIK3CA CCDS43171 aCa/aTa novel missense_variant ENST00000263967.3:c.2693C>T ENSP00000263967.3:p.Thr898Ile 0.999 probably damaging 0.02 deleterious 89 3.730 1.295 NA NA ENSG00000121879 ENST00000263967 ENSP00000263967 protein_coding 3_180430512 REFSEQ_P=NP_006209 | UNIPROT=P42336 | REFSEQ_T=NM_006218.2 | GENE_DESC=phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha [Source:HGNC Symbol;Acc:8975] | MIM_DESC= CONGENITAL LIPOMATOUS OVERGROWTH, VASCULAR MALFORMATIONS, AND EPIDERMAL; BREAST CANCER; HEPATOCELLULAR CARCINOMA; OVARIAN CANCER; KERATOSIS, SEBORRHEIC; COLORECTAL CANCER; CRC | UNIGENE=Hs.627302;Hs.633537;Hs.85701;Hs.715194;Hs.620758;Hs.553498 | MIM_ID=612918;114480;114550;167000;182000;114500
22
+ 5 137423570 T/G 1 10 0 T M124R G WNT8A NA aTg/aGg novel missense_variant ENST00000504809.1:c.371T>G ENSP00000424809.1:p.Met124Arg 0.69 possibly damaging 0.65 tolerated 91 4.650 2.471 NA NA ENSG00000061492 ENST00000504809 ENSP00000424809 protein_coding 5_137451469 REFSEQ_P= | UNIPROT= | REFSEQ_T= | GENE_DESC=wingless-type MMTV integration site family, member 8A [Source:HGNC Symbol;Acc:12788] | MIM_DESC= | UNIGENE=Hs.591274 | MIM_ID=
23
+ 5 137423570 T/G 1 10 0 T M106R G WNT8A NA aTg/aGg novel missense_variant ENST00000361560.2:c.317T>G ENSP00000354726.2:p.Met106Arg 0.456 possibly damaging 0.36 tolerated 91 4.650 2.471 NA NA ENSG00000061492 ENST00000361560 ENSP00000354726 protein_coding 5_137451469 REFSEQ_P= | UNIPROT=Q9H1J5 | REFSEQ_T= | GENE_DESC=wingless-type MMTV integration site family, member 8A [Source:HGNC Symbol;Acc:12788] | MIM_DESC= | UNIGENE=Hs.591274 | MIM_ID=
24
+ 5 137423570 T/G 1 10 0 T M106R G WNT8A CCDS43368 aTg/aGg novel missense_variant ENST00000398754.1:c.317T>G ENSP00000381739.1:p.Met106Arg 0.592 possibly damaging 0.41 tolerated 91 4.650 2.471 NA NA ENSG00000061492 ENST00000398754 ENSP00000381739 protein_coding 5_137451469 REFSEQ_P=NP_490645 | UNIPROT=Q9H1J5 | REFSEQ_T=NM_058244.2 | GENE_DESC=wingless-type MMTV integration site family, member 8A [Source:HGNC Symbol;Acc:12788] | MIM_DESC= | UNIGENE=Hs.591274 | MIM_ID=
25
+ 5 137423570 T/G 1 10 0 T M124R G WNT8A NA aTg/aGg novel missense_variant ENST00000506684.1:c.371T>G ENSP00000426653.1:p.Met124Arg 0.69 possibly damaging 0.52 tolerated 91 4.650 2.471 NA NA ENSG00000061492 ENST00000506684 ENSP00000426653 protein_coding 5_137451469 REFSEQ_P= | UNIPROT= | REFSEQ_T= | GENE_DESC=wingless-type MMTV integration site family, member 8A [Source:HGNC Symbol;Acc:12788] | MIM_DESC= | UNIGENE=Hs.591274 | MIM_ID=
26
+ 5 137423571 G/A 1 10 0 G M124I A WNT8A NA atG/atA novel missense_variant ENST00000504809.1:c.372G>A ENSP00000424809.1:p.Met124Ile 0.443 possibly damaging 0.16 tolerated 10 3.800 2.942 NA NA ENSG00000061492 ENST00000504809 ENSP00000424809 protein_coding 5_137451470 REFSEQ_P= | UNIPROT= | REFSEQ_T= | GENE_DESC=wingless-type MMTV integration site family, member 8A [Source:HGNC Symbol;Acc:12788] | MIM_DESC= | UNIGENE=Hs.591274 | MIM_ID=
27
+ 5 137423571 G/A 1 10 0 G M106I A WNT8A NA atG/atA novel missense_variant ENST00000361560.2:c.318G>A ENSP00000354726.2:p.Met106Ile 0.231 benign 0.05 tolerated 10 3.800 2.942 NA NA ENSG00000061492 ENST00000361560 ENSP00000354726 protein_coding 5_137451470 REFSEQ_P= | UNIPROT=Q9H1J5 | REFSEQ_T= | GENE_DESC=wingless-type MMTV integration site family, member 8A [Source:HGNC Symbol;Acc:12788] | MIM_DESC= | UNIGENE=Hs.591274 | MIM_ID=
28
+ 5 137423571 G/A 1 10 0 G M106I A WNT8A CCDS43368 atG/atA novel missense_variant ENST00000398754.1:c.318G>A ENSP00000381739.1:p.Met106Ile 0.341 benign 0.06 tolerated 10 3.800 2.942 NA NA ENSG00000061492 ENST00000398754 ENSP00000381739 protein_coding 5_137451470 REFSEQ_P=NP_490645 | UNIPROT=Q9H1J5 | REFSEQ_T=NM_058244.2 | GENE_DESC=wingless-type MMTV integration site family, member 8A [Source:HGNC Symbol;Acc:12788] | MIM_DESC= | UNIGENE=Hs.591274 | MIM_ID=
29
+ 5 137423571 G/A 1 10 0 G M124I A WNT8A NA atG/atA novel missense_variant ENST00000506684.1:c.372G>A ENSP00000426653.1:p.Met124Ile 0.443 possibly damaging 0.09 tolerated 10 3.800 2.942 NA NA ENSG00000061492 ENST00000506684 ENSP00000426653 protein_coding 5_137451470 REFSEQ_P= | UNIPROT= | REFSEQ_T= | GENE_DESC=wingless-type MMTV integration site family, member 8A [Source:HGNC Symbol;Acc:12788] | MIM_DESC= | UNIGENE=Hs.591274 | MIM_ID=
30
+ 6 138200252 C/T 1 17 0 C P557L T TNFAIP3 CCDS5187 cCt/cTt novel missense_variant ENST00000237289.4:c.1670C>T ENSP00000237289.4:p.Pro557Leu 0 benign 0.58 tolerated 98 3.280 1.179 NA NA ENSG00000118503 ENST00000237289 ENSP00000237289 protein_coding 6_138241945 REFSEQ_P=NP_001257437,NP_001257436,NP_006281 | UNIPROT=P21580 | REFSEQ_T=NM_001270508.1,NM_006290.3,NM_001270507.1 | GENE_DESC=tumor necrosis factor, alpha-induced protein 3 [Source:HGNC Symbol;Acc:11896] | MIM_DESC= | UNIGENE=Hs.211600;Hs.715063 | MIM_ID=
31
+ 8 37963909 G/A 1 11 0 G V68I A ASH2L NA Gtc/Atc novel missense_variant ENST00000517496.1:c.202G>A ENSP00000430889.1:p.Val68Ile 0.24 benign NA NA 29 3.740 1.735 NA NA ENSG00000129691 ENST00000517496 ENSP00000430889 protein_coding 8_38083066 REFSEQ_P= | UNIPROT= | REFSEQ_T= | GENE_DESC=ash2 (absent, small, or homeotic)-like (Drosophila) [Source:HGNC Symbol;Acc:744] | MIM_DESC= | UNIGENE=Hs.521530;Hs.608756 | MIM_ID=
32
+ 8 37963909 G/A 1 11 0 G V68I A ASH2L CCDS6101 Gtc/Atc novel missense_variant ENST00000343823.6:c.202G>A ENSP00000340896.5:p.Val68Ile 0.006 benign 0.7 tolerated 29 3.740 1.735 NA NA ENSG00000129691 ENST00000343823 ENSP00000340896 protein_coding 8_38083066 REFSEQ_P=NP_004665 | UNIPROT=Q9UBL3 | REFSEQ_T=NM_004674.4 | GENE_DESC=ash2 (absent, small, or homeotic)-like (Drosophila) [Source:HGNC Symbol;Acc:744] | MIM_DESC= | UNIGENE=Hs.521530;Hs.608756 | MIM_ID=
33
+ 10 123325072 C/T -1 13 0 C V86M T FGFR2 NA Gtg/Atg novel missense_variant ENST00000351936.6:c.256G>A ENSP00000309878.8:p.Val86Met 0.242 benign 0.21 tolerated 21 2.340 3.111 NA NA ENSG00000066468 ENST00000351936 ENSP00000309878 protein_coding 10_123315062 REFSEQ_P= | UNIPROT=P21802 | REFSEQ_T= | GENE_DESC=fibroblast growth factor receptor 2 [Source:HGNC Symbol;Acc:3689] | MIM_DESC= SCAPHOCEPHALY, MAXILLARY RETRUSION, AND MENTAL RETARDATION; LACRIMOAURICULODENTODIGITAL SYNDROME; LADD; BEARE-STEVENSON CUTIS GYRATA SYNDROME; BSTVS; BENT BONE DYSPLASIA SYNDROME; BBDS; PFEIFFER SYNDROME; ANTLEY-BIXLER SYNDROME WITHOUT GENITAL ANOMALIES OR DISORDERED STEROIDOGENESIS;; APERT SYNDROME; CROUZON SYNDROME; JACKSON-WEISS SYNDROME; JWS | UNIGENE=Hs.533683;Hs.607420;Hs.736928;Hs.622244 | MIM_ID=609579;149730;123790;614592;101600;207410;101200;123500;123150
34
+ 10 123325072 C/T -1 13 0 C V86M T FGFR2 NA Gtg/Atg novel missense_variant ENST00000346997.2:c.256G>A ENSP00000263451.5:p.Val86Met 0.256 benign 0.21 tolerated 21 2.340 3.111 NA NA ENSG00000066468 ENST00000346997 ENSP00000263451 protein_coding 10_123315062 REFSEQ_P= | UNIPROT=P21802 | REFSEQ_T= | GENE_DESC=fibroblast growth factor receptor 2 [Source:HGNC Symbol;Acc:3689] | MIM_DESC= SCAPHOCEPHALY, MAXILLARY RETRUSION, AND MENTAL RETARDATION; LACRIMOAURICULODENTODIGITAL SYNDROME; LADD; BEARE-STEVENSON CUTIS GYRATA SYNDROME; BSTVS; BENT BONE DYSPLASIA SYNDROME; BBDS; PFEIFFER SYNDROME; ANTLEY-BIXLER SYNDROME WITHOUT GENITAL ANOMALIES OR DISORDERED STEROIDOGENESIS;; APERT SYNDROME; CROUZON SYNDROME; JACKSON-WEISS SYNDROME; JWS | UNIGENE=Hs.533683;Hs.607420;Hs.736928;Hs.622244 | MIM_ID=609579;149730;123790;614592;101600;207410;101200;123500;123150
35
+ 10 123325072 C/T -1 13 0 C V86M T FGFR2 CCDS44486 Gtg/Atg novel missense_variant ENST00000369061.4:c.256G>A ENSP00000358057.4:p.Val86Met 0.77 possibly damaging 0.05 tolerated 21 2.340 3.111 NA NA ENSG00000066468 ENST00000369061 ENSP00000358057 protein_coding 10_123315062 REFSEQ_P=NP_001138386 | UNIPROT=P21802 | REFSEQ_T=NM_001144914.1 | GENE_DESC=fibroblast growth factor receptor 2 [Source:HGNC Symbol;Acc:3689] | MIM_DESC= SCAPHOCEPHALY, MAXILLARY RETRUSION, AND MENTAL RETARDATION; LACRIMOAURICULODENTODIGITAL SYNDROME; LADD; BEARE-STEVENSON CUTIS GYRATA SYNDROME; BSTVS; BENT BONE DYSPLASIA SYNDROME; BBDS; PFEIFFER SYNDROME; ANTLEY-BIXLER SYNDROME WITHOUT GENITAL ANOMALIES OR DISORDERED STEROIDOGENESIS;; APERT SYNDROME; CROUZON SYNDROME; JACKSON-WEISS SYNDROME; JWS | UNIGENE=Hs.533683;Hs.607420;Hs.736928;Hs.622244 | MIM_ID=609579;149730;123790;614592;101600;207410;101200;123500;123150
36
+ 10 123325072 C/T -1 13 0 C V86M T FGFR2 CCDS31298 Gtg/Atg novel missense_variant ENST00000358487.5:c.256G>A ENSP00000351276.5:p.Val86Met 0.355 benign 0.21 tolerated 21 2.340 3.111 NA NA ENSG00000066468 ENST00000358487 ENSP00000351276 protein_coding 10_123315062 REFSEQ_P=NP_000132 | UNIPROT=P21802 | REFSEQ_T=NM_000141.4 | GENE_DESC=fibroblast growth factor receptor 2 [Source:HGNC Symbol;Acc:3689] | MIM_DESC= SCAPHOCEPHALY, MAXILLARY RETRUSION, AND MENTAL RETARDATION; LACRIMOAURICULODENTODIGITAL SYNDROME; LADD; BEARE-STEVENSON CUTIS GYRATA SYNDROME; BSTVS; BENT BONE DYSPLASIA SYNDROME; BBDS; PFEIFFER SYNDROME; ANTLEY-BIXLER SYNDROME WITHOUT GENITAL ANOMALIES OR DISORDERED STEROIDOGENESIS;; APERT SYNDROME; CROUZON SYNDROME; JACKSON-WEISS SYNDROME; JWS | UNIGENE=Hs.533683;Hs.607420;Hs.736928;Hs.622244 | MIM_ID=609579;149730;123790;614592;101600;207410;101200;123500;123150
37
+ 10 123325072 C/T -1 13 0 C V86M T FGFR2 NA Gtg/Atg novel missense_variant ENST00000359354.2:c.256G>A ENSP00000352309.2:p.Val86Met 0.724 possibly damaging 0.23 tolerated 21 2.340 3.111 NA NA ENSG00000066468 ENST00000359354 ENSP00000352309 protein_coding 10_123315062 REFSEQ_P= | UNIPROT=P21802 | REFSEQ_T= | GENE_DESC=fibroblast growth factor receptor 2 [Source:HGNC Symbol;Acc:3689] | MIM_DESC= SCAPHOCEPHALY, MAXILLARY RETRUSION, AND MENTAL RETARDATION; LACRIMOAURICULODENTODIGITAL SYNDROME; LADD; BEARE-STEVENSON CUTIS GYRATA SYNDROME; BSTVS; BENT BONE DYSPLASIA SYNDROME; BBDS; PFEIFFER SYNDROME; ANTLEY-BIXLER SYNDROME WITHOUT GENITAL ANOMALIES OR DISORDERED STEROIDOGENESIS;; APERT SYNDROME; CROUZON SYNDROME; JACKSON-WEISS SYNDROME; JWS | UNIGENE=Hs.533683;Hs.607420;Hs.736928;Hs.622244 | MIM_ID=609579;149730;123790;614592;101600;207410;101200;123500;123150
38
+ 10 123325072 C/T -1 13 0 C V86M T FGFR2 NA Gtg/Atg novel missense_variant ENST00000369058.3:c.256G>A ENSP00000358054.3:p.Val86Met 0.242 benign 0.21 tolerated 21 2.340 3.111 NA NA ENSG00000066468 ENST00000369058 ENSP00000358054 protein_coding 10_123315062 REFSEQ_P= | UNIPROT=P21802 | REFSEQ_T= | GENE_DESC=fibroblast growth factor receptor 2 [Source:HGNC Symbol;Acc:3689] | MIM_DESC= SCAPHOCEPHALY, MAXILLARY RETRUSION, AND MENTAL RETARDATION; LACRIMOAURICULODENTODIGITAL SYNDROME; LADD; BEARE-STEVENSON CUTIS GYRATA SYNDROME; BSTVS; BENT BONE DYSPLASIA SYNDROME; BBDS; PFEIFFER SYNDROME; ANTLEY-BIXLER SYNDROME WITHOUT GENITAL ANOMALIES OR DISORDERED STEROIDOGENESIS;; APERT SYNDROME; CROUZON SYNDROME; JACKSON-WEISS SYNDROME; JWS | UNIGENE=Hs.533683;Hs.607420;Hs.736928;Hs.622244 | MIM_ID=609579;149730;123790;614592;101600;207410;101200;123500;123150
39
+ 10 123325072 C/T -1 13 0 C V86M T FGFR2 CCDS44487 Gtg/Atg novel missense_variant ENST00000369060.4:c.256G>A ENSP00000358056.4:p.Val86Met 0.88 possibly damaging 0.07 tolerated 21 2.340 3.111 NA NA ENSG00000066468 ENST00000369060 ENSP00000358056 protein_coding 10_123315062 REFSEQ_P=NP_001138389 | UNIPROT=P21802 | REFSEQ_T=NM_001144917.1 | GENE_DESC=fibroblast growth factor receptor 2 [Source:HGNC Symbol;Acc:3689] | MIM_DESC= SCAPHOCEPHALY, MAXILLARY RETRUSION, AND MENTAL RETARDATION; LACRIMOAURICULODENTODIGITAL SYNDROME; LADD; BEARE-STEVENSON CUTIS GYRATA SYNDROME; BSTVS; BENT BONE DYSPLASIA SYNDROME; BBDS; PFEIFFER SYNDROME; ANTLEY-BIXLER SYNDROME WITHOUT GENITAL ANOMALIES OR DISORDERED STEROIDOGENESIS;; APERT SYNDROME; CROUZON SYNDROME; JACKSON-WEISS SYNDROME; JWS | UNIGENE=Hs.533683;Hs.607420;Hs.736928;Hs.622244 | MIM_ID=609579;149730;123790;614592;101600;207410;101200;123500;123150
40
+ 10 123325072 C/T -1 13 0 C V86M T FGFR2 CCDS44489 Gtg/Atg novel missense_variant ENST00000369056.1:c.256G>A ENSP00000358052.1:p.Val86Met 0.421 benign 0.21 tolerated 21 2.340 3.111 NA NA ENSG00000066468 ENST00000369056 ENSP00000358052 protein_coding 10_123315062 REFSEQ_P=NP_001138385 | UNIPROT=P21802 | REFSEQ_T=NM_001144913.1 | GENE_DESC=fibroblast growth factor receptor 2 [Source:HGNC Symbol;Acc:3689] | MIM_DESC= SCAPHOCEPHALY, MAXILLARY RETRUSION, AND MENTAL RETARDATION; LACRIMOAURICULODENTODIGITAL SYNDROME; LADD; BEARE-STEVENSON CUTIS GYRATA SYNDROME; BSTVS; BENT BONE DYSPLASIA SYNDROME; BBDS; PFEIFFER SYNDROME; ANTLEY-BIXLER SYNDROME WITHOUT GENITAL ANOMALIES OR DISORDERED STEROIDOGENESIS;; APERT SYNDROME; CROUZON SYNDROME; JACKSON-WEISS SYNDROME; JWS | UNIGENE=Hs.533683;Hs.607420;Hs.736928;Hs.622244 | MIM_ID=609579;149730;123790;614592;101600;207410;101200;123500;123150
41
+ 10 123325072 C/T -1 13 0 C V86M T FGFR2 CCDS7620 Gtg/Atg novel missense_variant ENST00000457416.2:c.256G>A ENSP00000410294.2:p.Val86Met 0.242 benign 0.21 tolerated 21 2.340 3.111 NA NA ENSG00000066468 ENST00000457416 ENSP00000410294 protein_coding 10_123315062 REFSEQ_P=NP_075259 | UNIPROT=P21802 | REFSEQ_T=NM_022970.3 | GENE_DESC=fibroblast growth factor receptor 2 [Source:HGNC Symbol;Acc:3689] | MIM_DESC= SCAPHOCEPHALY, MAXILLARY RETRUSION, AND MENTAL RETARDATION; LACRIMOAURICULODENTODIGITAL SYNDROME; LADD; BEARE-STEVENSON CUTIS GYRATA SYNDROME; BSTVS; BENT BONE DYSPLASIA SYNDROME; BBDS; PFEIFFER SYNDROME; ANTLEY-BIXLER SYNDROME WITHOUT GENITAL ANOMALIES OR DISORDERED STEROIDOGENESIS;; APERT SYNDROME; CROUZON SYNDROME; JACKSON-WEISS SYNDROME; JWS | UNIGENE=Hs.533683;Hs.607420;Hs.736928;Hs.622244 | MIM_ID=609579;149730;123790;614592;101600;207410;101200;123500;123150
42
+ 11 66481177 C/T -1 9 0 C A233T T SPTBN2 CCDS8150 Gca/Aca novel missense_variant ENST00000533211.1:c.697G>A ENSP00000432568.1:p.Ala233Thr 0.862 possibly damaging 0.01 deleterious 58 4.570 0.527 NA NA ENSG00000173898 ENST00000533211 ENSP00000432568 protein_coding 11_66237753 REFSEQ_P= | UNIPROT=O15020 | REFSEQ_T= | GENE_DESC=spectrin, beta, non-erythrocytic 2 [Source:HGNC Symbol;Acc:11276] | MIM_DESC= SPINOCEREBELLAR ATAXIA 5; SCA5 | UNIGENE=Hs.600552;Hs.26915 | MIM_ID=600224
43
+ 11 66481177 C/T -1 9 0 C A233T T SPTBN2 NA Gca/Aca novel missense_variant ENST00000529997.1:c.697G>A ENSP00000433593.1:p.Ala233Thr 0.664 possibly damaging 0.01 deleterious 58 4.570 0.527 NA NA ENSG00000173898 ENST00000529997 ENSP00000433593 protein_coding 11_66237753 REFSEQ_P= | UNIPROT=O15020 | REFSEQ_T= | GENE_DESC=spectrin, beta, non-erythrocytic 2 [Source:HGNC Symbol;Acc:11276] | MIM_DESC= SPINOCEREBELLAR ATAXIA 5; SCA5 | UNIGENE=Hs.600552;Hs.26915 | MIM_ID=600224
44
+ 11 66481177 C/T -1 9 0 C A233T T SPTBN2 CCDS8150 Gca/Aca novel missense_variant ENST00000309996.2:c.697G>A ENSP00000311489.2:p.Ala233Thr 0.862 possibly damaging 0.01 deleterious 58 4.570 0.527 NA NA ENSG00000173898 ENST00000309996 ENSP00000311489 protein_coding 11_66237753 REFSEQ_P=NP_008877 | UNIPROT=O15020 | REFSEQ_T=NM_006946.2 | GENE_DESC=spectrin, beta, non-erythrocytic 2 [Source:HGNC Symbol;Acc:11276] | MIM_DESC= SPINOCEREBELLAR ATAXIA 5; SCA5 | UNIGENE=Hs.600552;Hs.26915 | MIM_ID=600224
45
+ 12 69218140 C/T 1 11 0 C NA T MDM2 NA NA novel splice_region_variant ENST00000393415.3:c.341-3C>T NA NA NA NA NA NA 1.180 0.877 NA NA ENSG00000135679 ENST00000393415 ENSP00000377067 protein_coding 12_67504407 REFSEQ_P= | UNIPROT= | REFSEQ_T= | GENE_DESC=MDM2 oncogene, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:6973] | MIM_DESC= ACCELERATED TUMOR FORMATION, SUSCEPTIBILITY TO; ACTFS | UNIGENE=Hs.658568;Hs.484551 | MIM_ID=614401
46
+ 12 69218140 C/T 1 11 0 C NA T MDM2 NA NA novel splice_region_variant ENST00000393416.2:c.434-3C>T NA NA NA NA NA NA 1.180 0.877 NA NA ENSG00000135679 ENST00000393416 ENSP00000377068 protein_coding 12_67504407 REFSEQ_P= | UNIPROT= | REFSEQ_T= | GENE_DESC=MDM2 oncogene, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:6973] | MIM_DESC= ACCELERATED TUMOR FORMATION, SUSCEPTIBILITY TO; ACTFS | UNIGENE=Hs.658568;Hs.484551 | MIM_ID=614401
47
+ 12 69218140 C/T 1 11 0 C NA T MDM2 NA NA novel splice_region_variant ENST00000546048.1:c.207-3C>T NA NA NA NA NA NA 1.180 0.877 NA NA ENSG00000135679 ENST00000546048 ENSP00000445222 protein_coding 12_67504407 REFSEQ_P= | UNIPROT= | REFSEQ_T= | GENE_DESC=MDM2 oncogene, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:6973] | MIM_DESC= ACCELERATED TUMOR FORMATION, SUSCEPTIBILITY TO; ACTFS | UNIGENE=Hs.658568;Hs.484551 | MIM_ID=614401
48
+ 12 69218140 C/T 1 11 0 C NA T MDM2 NA NA novel splice_region_variant ENST00000537182.1:c.207-3C>T NA NA NA NA NA NA 1.180 0.877 NA NA ENSG00000135679 ENST00000537182 ENSP00000443450 protein_coding 12_67504407 REFSEQ_P= | UNIPROT= | REFSEQ_T= | GENE_DESC=MDM2 oncogene, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:6973] | MIM_DESC= ACCELERATED TUMOR FORMATION, SUSCEPTIBILITY TO; ACTFS | UNIGENE=Hs.658568;Hs.484551 | MIM_ID=614401
49
+ 12 69218140 C/T 1 11 0 C NA T MDM2 NA NA novel splice_region_variant ENST00000540352.1:c.341-3C>T NA NA NA NA NA NA 1.180 0.877 NA NA ENSG00000135679 ENST00000540352 ENSP00000445030 protein_coding 12_67504407 REFSEQ_P= | UNIPROT= | REFSEQ_T= | GENE_DESC=MDM2 oncogene, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:6973] | MIM_DESC= ACCELERATED TUMOR FORMATION, SUSCEPTIBILITY TO; ACTFS | UNIGENE=Hs.658568;Hs.484551 | MIM_ID=614401
50
+ 12 69218140 C/T 1 11 0 C NA T MDM2 NA NA novel splice_region_variant ENST00000350057.5:c.266-3C>T NA NA NA NA NA NA 1.180 0.877 NA NA ENSG00000135679 ENST00000350057 ENSP00000266624 protein_coding 12_67504407 REFSEQ_P= | UNIPROT= | REFSEQ_T= | GENE_DESC=MDM2 oncogene, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:6973] | MIM_DESC= ACCELERATED TUMOR FORMATION, SUSCEPTIBILITY TO; ACTFS | UNIGENE=Hs.658568;Hs.484551 | MIM_ID=614401
51
+ 12 69218140 C/T 1 11 0 C NA T MDM2 CCDS8986 NA novel splice_region_variant ENST00000462284.1:c.359-3C>T NA NA NA NA NA NA 1.180 0.877 NA NA ENSG00000135679 ENST00000462284 ENSP00000417281 protein_coding 12_67504407 REFSEQ_P=NP_002383 | UNIPROT=Q00987 | REFSEQ_T=NM_002392.4 | GENE_DESC=MDM2 oncogene, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:6973] | MIM_DESC= ACCELERATED TUMOR FORMATION, SUSCEPTIBILITY TO; ACTFS | UNIGENE=Hs.658568;Hs.484551 | MIM_ID=614401
52
+ 12 69218140 C/T 1 11 0 C NA T MDM2 NA NA novel splice_region_variant ENST00000311420.9:c.225-3C>T NA NA NA NA NA NA 1.180 0.877 NA NA ENSG00000135679 ENST00000311420 ENSP00000310742 protein_coding 12_67504407 REFSEQ_P= | UNIPROT= | REFSEQ_T= | GENE_DESC=MDM2 oncogene, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:6973] | MIM_DESC= ACCELERATED TUMOR FORMATION, SUSCEPTIBILITY TO; ACTFS | UNIGENE=Hs.658568;Hs.484551 | MIM_ID=614401
53
+ 12 69218140 C/T 1 11 0 C NA T MDM2 NA NA novel splice_region_variant ENST00000539479.1:c.341-3C>T NA NA NA NA NA NA 1.180 0.877 NA NA ENSG00000135679 ENST00000539479 ENSP00000444430 protein_coding 12_67504407 REFSEQ_P= | UNIPROT= | REFSEQ_T= | GENE_DESC=MDM2 oncogene, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:6973] | MIM_DESC= ACCELERATED TUMOR FORMATION, SUSCEPTIBILITY TO; ACTFS | UNIGENE=Hs.658568;Hs.484551 | MIM_ID=614401
54
+ 12 69218140 C/T 1 11 0 C NA T MDM2 NA NA novel splice_region_variant ENST00000496959.1:c.157-3C>T NA NA NA NA NA NA 1.180 0.877 NA NA ENSG00000135679 ENST00000496959 ENSP00000429692 protein_coding 12_67504407 REFSEQ_P= | UNIPROT= | REFSEQ_T= | GENE_DESC=MDM2 oncogene, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:6973] | MIM_DESC= ACCELERATED TUMOR FORMATION, SUSCEPTIBILITY TO; ACTFS | UNIGENE=Hs.658568;Hs.484551 | MIM_ID=614401
55
+ 12 69218140 C/T 1 11 0 C NA T MDM2 NA NA novel splice_region_variant ENST00000481186.1:c.82-3C>T NA NA NA NA NA NA 1.180 0.877 NA NA ENSG00000135679 ENST00000481186 ENSP00000431110 protein_coding 12_67504407 REFSEQ_P= | UNIPROT= | REFSEQ_T= | GENE_DESC=MDM2 oncogene, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:6973] | MIM_DESC= ACCELERATED TUMOR FORMATION, SUSCEPTIBILITY TO; ACTFS | UNIGENE=Hs.658568;Hs.484551 | MIM_ID=614401
56
+ 12 69218140 C/T 1 11 0 C NA T MDM2 NA NA novel splice_region_variant ENST00000393417.3:c.*215-3C>T NA NA NA NA NA NA 1.180 0.877 NA NA ENSG00000135679 ENST00000393417 ENSP00000429021 protein_coding 12_67504407 REFSEQ_P= | UNIPROT= | REFSEQ_T= | GENE_DESC=MDM2 oncogene, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:6973] | MIM_DESC= ACCELERATED TUMOR FORMATION, SUSCEPTIBILITY TO; ACTFS | UNIGENE=Hs.658568;Hs.484551 | MIM_ID=614401
57
+ 12 69218140 C/T 1 11 0 C NA T MDM2 NA NA novel splice_region_variant ENST00000536089.1:c.207-3C>T NA NA NA NA NA NA 1.180 0.877 NA NA ENSG00000135679 ENST00000536089 ENSP00000444028 protein_coding 12_67504407 REFSEQ_P= | UNIPROT= | REFSEQ_T= | GENE_DESC=MDM2 oncogene, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:6973] | MIM_DESC= ACCELERATED TUMOR FORMATION, SUSCEPTIBILITY TO; ACTFS | UNIGENE=Hs.658568;Hs.484551 | MIM_ID=614401
58
+ 13 28971139 T/C -1 10 0 T K540E C FLT1 CCDS9330 Aaa/Gaa novel missense_variant ENST00000282397.4:c.1618A>G ENSP00000282397.4:p.Lys540Glu 0.288 benign 0.02 deleterious 56 4.200 2.553 NA NA ENSG00000102755 ENST00000282397 ENSP00000282397 protein_coding 13_27869139 REFSEQ_P=NP_001153392,NP_002010 | UNIPROT=P17948 | REFSEQ_T=NM_002019.4 | GENE_DESC=fms-related tyrosine kinase 1 [Source:HGNC Symbol;Acc:3763] | MIM_DESC= | UNIGENE=Hs.658796;Hs.594454 | MIM_ID=
59
+ 13 28971139 T/C -1 10 0 T K540E C FLT1 CCDS53860 Aaa/Gaa novel missense_variant ENST00000541932.1:c.1618A>G ENSP00000437631.1:p.Lys540Glu 0.908 probably damaging 0.03 deleterious 56 4.200 2.553 NA NA ENSG00000102755 ENST00000541932 ENSP00000437631 protein_coding 13_27869139 REFSEQ_P=NP_001153392,NP_001153502 | UNIPROT=P17948 | REFSEQ_T=NM_001160030.1 | GENE_DESC=fms-related tyrosine kinase 1 [Source:HGNC Symbol;Acc:3763] | MIM_DESC= | UNIGENE=Hs.658796;Hs.594454 | MIM_ID=
60
+ 14 91365722 C/T -1 11 0 C C475Y T RPS6KA5 CCDS9893 tGt/tAt novel missense_variant ENST00000261991.3:c.1424G>A ENSP00000261991.3:p.Cys475Tyr 1 probably damaging 0.29 tolerated 194 4.500 2.831 NA NA ENSG00000100784 ENST00000261991 ENSP00000261991 protein_coding 14_90435475 REFSEQ_P=NP_004746 | UNIPROT=O75582 | REFSEQ_T=NM_004755.2 | GENE_DESC=ribosomal protein S6 kinase, 90kDa, polypeptide 5 [Source:HGNC Symbol;Acc:10434] | MIM_DESC= | UNIGENE=Hs.733807 | MIM_ID=
61
+ 14 91365722 C/T -1 11 0 C C475Y T RPS6KA5 CCDS45149 tGt/tAt novel missense_variant ENST00000418736.2:c.1424G>A ENSP00000402787.2:p.Cys475Tyr 0.999 probably damaging 0.27 tolerated 194 4.500 2.831 NA NA ENSG00000100784 ENST00000418736 ENSP00000402787 protein_coding 14_90435475 REFSEQ_P=NP_872198 | UNIPROT=O75582 | REFSEQ_T=NM_182398.1 | GENE_DESC=ribosomal protein S6 kinase, 90kDa, polypeptide 5 [Source:HGNC Symbol;Acc:10434] | MIM_DESC= | UNIGENE=Hs.733807 | MIM_ID=
62
+ 14 91365722 C/T -1 11 0 C C396Y T RPS6KA5 NA tGt/tAt novel missense_variant ENST00000536315.2:c.1187G>A ENSP00000442803.2:p.Cys396Tyr 1 probably damaging 0.17 tolerated 194 4.500 2.831 NA NA ENSG00000100784 ENST00000536315 ENSP00000442803 protein_coding 14_90435475 REFSEQ_P= | UNIPROT= | REFSEQ_T= | GENE_DESC=ribosomal protein S6 kinase, 90kDa, polypeptide 5 [Source:HGNC Symbol;Acc:10434] | MIM_DESC= | UNIGENE=Hs.733807 | MIM_ID=
63
+ 15 50884738 T/C -1 11 0 T I1232V C TRPM7 NA Att/Gtt novel missense_variant ENST00000560955.1:c.3694A>G ENSP00000453277.1:p.Ile1232Val 0.051 benign 0.35 tolerated 29 3.440 2.973 NA NA ENSG00000092439 ENST00000560955 ENSP00000453277 protein_coding 15_48672030 REFSEQ_P= | UNIPROT= | REFSEQ_T= | GENE_DESC=transient receptor potential cation channel, subfamily M, member 7 [Source:HGNC Symbol;Acc:17994] | MIM_DESC= AMYOTROPHIC LATERAL SCLEROSIS-PARKINSONISM/DEMENTIA COMPLEX 1 | UNIGENE=Hs.734904;Hs.512894 | MIM_ID=105500
64
+ 15 50884738 T/C -1 11 0 T I1232V C TRPM7 CCDS42035 Att/Gtt novel missense_variant ENST00000313478.7:c.3694A>G ENSP00000320239.7:p.Ile1232Val 0.029 benign 0.35 tolerated 29 3.440 2.973 NA NA ENSG00000092439 ENST00000313478 ENSP00000320239 protein_coding 15_48672030 REFSEQ_P=NP_060142 | UNIPROT=Q96QT4 | REFSEQ_T=NM_017672.4 | GENE_DESC=transient receptor potential cation channel, subfamily M, member 7 [Source:HGNC Symbol;Acc:17994] | MIM_DESC= AMYOTROPHIC LATERAL SCLEROSIS-PARKINSONISM/DEMENTIA COMPLEX 1 | UNIGENE=Hs.734904;Hs.512894 | MIM_ID=105500
65
+ 15 64332378 T/C -1 11 0 T E28G C DAPK2 NA gAg/gGg novel missense_variant ENST00000559306.1:c.83A>G ENSP00000452970.1:p.Glu28Gly 0.56 possibly damaging 0.08 tolerated 98 4.360 3.967 NA NA ENSG00000035664 ENST00000559306 ENSP00000452970 protein_coding 15_62119431 REFSEQ_P= | UNIPROT= | REFSEQ_T= | GENE_DESC=death-associated protein kinase 2 [Source:HGNC Symbol;Acc:2675] | MIM_DESC= | UNIGENE=Hs.237886;Hs.603282;Hs.623561 | MIM_ID=
66
+ 15 64332378 T/C -1 11 0 T E28G C DAPK2 CCDS10188 gAg/gGg novel missense_variant ENST00000457488.1:c.83A>G ENSP00000408277.1:p.Glu28Gly 0.56 possibly damaging 0.12 tolerated 98 4.360 3.967 NA NA ENSG00000035664 ENST00000457488 ENSP00000408277 protein_coding 15_62119431 REFSEQ_P=NP_055141 | UNIPROT=Q9UIK4 | REFSEQ_T=NM_014326.3 | GENE_DESC=death-associated protein kinase 2 [Source:HGNC Symbol;Acc:2675] | MIM_DESC= | UNIGENE=Hs.237886;Hs.603282;Hs.623561 | MIM_ID=
67
+ 15 64332378 T/C -1 11 0 T E28G C DAPK2 NA gAg/gGg novel missense_variant ENST00000558069.1:c.83A>G ENSP00000453235.1:p.Glu28Gly 0.292 benign 0.01 deleterious 98 4.360 3.967 NA NA ENSG00000035664 ENST00000558069 ENSP00000453235 protein_coding 15_62119431 REFSEQ_P= | UNIPROT= | REFSEQ_T= | GENE_DESC=death-associated protein kinase 2 [Source:HGNC Symbol;Acc:2675] | MIM_DESC= | UNIGENE=Hs.237886;Hs.603282;Hs.623561 | MIM_ID=
68
+ 15 64332378 T/C -1 11 0 T E28G C DAPK2 CCDS10188 gAg/gGg novel missense_variant ENST00000261891.3:c.83A>G ENSP00000261891.3:p.Glu28Gly 0.56 possibly damaging 0.12 tolerated 98 4.360 3.967 NA NA ENSG00000035664 ENST00000261891 ENSP00000261891 protein_coding 15_62119431 REFSEQ_P= | UNIPROT=Q9UIK4 | REFSEQ_T= | GENE_DESC=death-associated protein kinase 2 [Source:HGNC Symbol;Acc:2675] | MIM_DESC= | UNIGENE=Hs.237886;Hs.603282;Hs.623561 | MIM_ID=
69
+ 15 64332378 T/C -1 11 0 T E28G C DAPK2 NA gAg/gGg novel missense_variant ENST00000561162.1:c.83A>G ENSP00000453284.1:p.Glu28Gly 0 unknown NA NA 98 4.360 3.967 NA NA ENSG00000035664 ENST00000561162 ENSP00000453284 protein_coding 15_62119431 REFSEQ_P= | UNIPROT= | REFSEQ_T= | GENE_DESC=death-associated protein kinase 2 [Source:HGNC Symbol;Acc:2675] | MIM_DESC= | UNIGENE=Hs.237886;Hs.603282;Hs.623561 | MIM_ID=
70
+ 15 64332378 T/C -1 11 0 T E28G C DAPK2 NA gAg/gGg novel missense_variant ENST00000559007.1:c.83A>G ENSP00000453639.1:p.Glu28Gly 0.761 possibly damaging 0.01 deleterious 98 4.360 3.967 NA NA ENSG00000035664 ENST00000559007 ENSP00000453639 protein_coding 15_62119431 REFSEQ_P= | UNIPROT= | REFSEQ_T= | GENE_DESC=death-associated protein kinase 2 [Source:HGNC Symbol;Acc:2675] | MIM_DESC= | UNIGENE=Hs.237886;Hs.603282;Hs.623561 | MIM_ID=
71
+ 17 38787079 T/C -1 16 0 T -289- C SMARCE1 NA aA/aG novel incomplete_terminal_codon_variant ENST00000478349.2:c.866A>G ENST00000478349.2:c.866A>G(p.=) NA NA NA NA NA 3.410 3.072 NA NA ENSG00000073584 ENST00000478349 ENSP00000463216 protein_coding 17_36040605 REFSEQ_P= | UNIPROT= | REFSEQ_T= | GENE_DESC=SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1 [Source:HGNC Symbol;Acc:11109] | MIM_DESC= | UNIGENE=Hs.743978 | MIM_ID=
72
+ 17 38787079 T/C -1 16 0 T K235R C SMARCE1 NA aAg/aGg novel missense_variant ENST00000544009.1:c.704A>G ENSP00000441857.1:p.Lys235Arg 0.003 benign 0.42 tolerated 26 3.410 3.072 NA NA ENSG00000073584 ENST00000544009 ENSP00000441857 protein_coding 17_36040605 REFSEQ_P= | UNIPROT= | REFSEQ_T= | GENE_DESC=SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1 [Source:HGNC Symbol;Acc:11109] | MIM_DESC= | UNIGENE=Hs.743978 | MIM_ID=
73
+ 17 38787079 T/C -1 16 0 T K287R C SMARCE1 NA aAg/aGg novel missense_variant ENST00000431889.2:c.860A>G ENSP00000445370.1:p.Lys287Arg 0.003 benign 0.5 tolerated 26 3.410 3.072 NA NA ENSG00000073584 ENST00000431889 ENSP00000445370 protein_coding 17_36040605 REFSEQ_P= | UNIPROT= | REFSEQ_T= | GENE_DESC=SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1 [Source:HGNC Symbol;Acc:11109] | MIM_DESC= | UNIGENE=Hs.743978 | MIM_ID=
74
+ 17 38787079 T/C -1 16 0 T K235R C SMARCE1 NA aAg/aGg novel missense_variant ENST00000400122.3:c.704A>G ENSP00000411607.2:p.Lys235Arg 0.043 benign 0.17 tolerated 26 3.410 3.072 NA NA ENSG00000073584 ENST00000400122 ENSP00000411607 protein_coding 17_36040605 REFSEQ_P= | UNIPROT= | REFSEQ_T= | GENE_DESC=SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1 [Source:HGNC Symbol;Acc:11109] | MIM_DESC= | UNIGENE=Hs.743978 | MIM_ID=
75
+ 17 38787079 T/C -1 16 0 T K270R C SMARCE1 NA aAg/aGg novel missense_variant ENST00000377808.4:c.809A>G ENSP00000367039.4:p.Lys270Arg 0.043 benign 0.16 tolerated 26 3.410 3.072 NA NA ENSG00000073584 ENST00000377808 ENSP00000367039 protein_coding 17_36040605 REFSEQ_P= | UNIPROT= | REFSEQ_T= | GENE_DESC=SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1 [Source:HGNC Symbol;Acc:11109] | MIM_DESC= | UNIGENE=Hs.743978 | MIM_ID=
76
+ 17 38787079 T/C -1 16 0 T K99R C SMARCE1 NA aAg/aGg novel missense_variant ENST00000447024.1:c.296A>G ENSP00000392958.1:p.Lys99Arg 0.043 benign 0.1 tolerated 26 3.410 3.072 NA NA ENSG00000073584 ENST00000447024 ENSP00000392958 protein_coding 17_36040605 REFSEQ_P= | UNIPROT= | REFSEQ_T= | GENE_DESC=SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1 [Source:HGNC Symbol;Acc:11109] | MIM_DESC= | UNIGENE=Hs.743978 | MIM_ID=
77
+ 17 38787079 T/C -1 16 0 T K305R C SMARCE1 CCDS11370 aAg/aGg novel missense_variant ENST00000348513.6:c.914A>G ENSP00000323967.6:p.Lys305Arg 0.003 benign 0.41 tolerated 26 3.410 3.072 NA NA ENSG00000073584 ENST00000348513 ENSP00000323967 protein_coding 17_36040605 REFSEQ_P=NP_003070 | UNIPROT=Q969G3 | REFSEQ_T=NM_003079.4 | GENE_DESC=SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1 [Source:HGNC Symbol;Acc:11109] | MIM_DESC= | UNIGENE=Hs.743978 | MIM_ID=
78
+ 17 38787079 T/C -1 16 0 T K119R C SMARCE1 NA aAg/aGg novel missense_variant ENST00000264640.4:c.354A>G ENSP00000466608.1:p.Lys119Arg 0.349 benign 0.24 tolerated 26 3.410 3.072 NA NA ENSG00000073584 ENST00000264640 ENSP00000466608 protein_coding 17_36040605 REFSEQ_P= | UNIPROT= | REFSEQ_T= | GENE_DESC=SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1 [Source:HGNC Symbol;Acc:11109] | MIM_DESC= | UNIGENE=Hs.743978 | MIM_ID=
79
+ 17 38787079 T/C -1 16 0 T K270R C SMARCE1 NA aAg/aGg novel missense_variant ENST00000580419.1:c.809A>G ENSP00000462475.1:p.Lys270Arg 0 benign 0.4 tolerated 26 3.410 3.072 NA NA ENSG00000073584 ENST00000580419 ENSP00000462475 protein_coding 17_36040605 REFSEQ_P= | UNIPROT= | REFSEQ_T= | GENE_DESC=SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1 [Source:HGNC Symbol;Acc:11109] | MIM_DESC= | UNIGENE=Hs.743978 | MIM_ID=
80
+ 17 38787079 T/C -1 16 0 T K235R C SMARCE1 NA aAg/aGg novel missense_variant ENST00000578044.1:c.704A>G ENSP00000464511.1:p.Lys235Arg 0.003 benign 0.42 tolerated 26 3.410 3.072 NA NA ENSG00000073584 ENST00000578044 ENSP00000464511 protein_coding 17_36040605 REFSEQ_P= | UNIPROT= | REFSEQ_T= | GENE_DESC=SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1 [Source:HGNC Symbol;Acc:11109] | MIM_DESC= | UNIGENE=Hs.743978 | MIM_ID=
81
+ 17 56676661 G/T -1 22 0 G S682* T TEX14 CCDS32692 tCa/tAa novel stop_gained ENST00000349033.5:c.2045C>A ENSP00000268910.8:p.Ser682Ter NA NA NA NA NA 3.140 1.174 NA NA ENSG00000121101 ENST00000349033 ENSP00000268910 protein_coding 17_54031660 REFSEQ_P=NP_112562 | UNIPROT=Q8IWB6 | REFSEQ_T=NM_031272.4 | GENE_DESC=testis expressed 14 [Source:HGNC Symbol;Acc:11737] | MIM_DESC= | UNIGENE=Hs.390221 | MIM_ID=
82
+ 17 56676661 G/T -1 22 0 G S682* T TEX14 CCDS32693 tCa/tAa novel stop_gained ENST00000389934.3:c.2045C>A ENSP00000374584.3:p.Ser682Ter NA NA NA NA NA 3.140 1.174 NA NA ENSG00000121101 ENST00000389934 ENSP00000374584 protein_coding 17_54031660 REFSEQ_P=NP_001188386,NP_938207 | UNIPROT=Q8IWB6 | REFSEQ_T=NM_198393.3,NM_001201457.1 | GENE_DESC=testis expressed 14 [Source:HGNC Symbol;Acc:11737] | MIM_DESC= | UNIGENE=Hs.390221 | MIM_ID=
83
+ 17 56676661 G/T -1 22 0 G S688* T TEX14 CCDS56042 tCa/tAa novel stop_gained ENST00000240361.8:c.2063C>A ENSP00000240361.8:p.Ser688Ter NA NA NA NA NA 3.140 1.174 NA NA ENSG00000121101 ENST00000240361 ENSP00000240361 protein_coding 17_54031660 REFSEQ_P= | UNIPROT=Q8IWB6 | REFSEQ_T= | GENE_DESC=testis expressed 14 [Source:HGNC Symbol;Acc:11737] | MIM_DESC= | UNIGENE=Hs.390221 | MIM_ID=
84
+ 17 58011552 T/C 1 15 0 T F237S C RPS6KB1 NA tTt/tCt novel missense_variant ENST00000406116.3:c.710T>C ENSP00000384335.3:p.Phe237Ser 1 probably damaging 0 deleterious 155 NA NA NA NA ENSG00000108443 ENST00000406116 ENSP00000384335 protein_coding 17_55366334 REFSEQ_P=NP_001258972 | UNIPROT= | REFSEQ_T= | GENE_DESC=ribosomal protein S6 kinase, 70kDa, polypeptide 1 [Source:HGNC Symbol;Acc:10436] | MIM_DESC= | UNIGENE=Hs.706493;Hs.613833;Hs.568211;Hs.463642;Hs.604293;Hs.601380 | MIM_ID=
85
+ 17 58011552 T/C 1 15 0 T F237S C RPS6KB1 CCDS11621 tTt/tCt novel missense_variant ENST00000225577.4:c.710T>C ENSP00000225577.4:p.Phe237Ser 1 probably damaging 0 deleterious 155 NA NA NA NA ENSG00000108443 ENST00000225577 ENSP00000225577 protein_coding 17_55366334 REFSEQ_P=NP_001258973,NP_001258971,NP_001258989,NP_003152 | UNIPROT=P23443 | REFSEQ_T=NM_001272060.1(identity=97%/97%),NM_001272044.1(identity=94%/92%),NM_003161.2,NM_001272042.1(identity=90%/91%) | GENE_DESC=ribosomal protein S6 kinase, 70kDa, polypeptide 1 [Source:HGNC Symbol;Acc:10436] | MIM_DESC= | UNIGENE=Hs.706493;Hs.613833;Hs.568211;Hs.463642;Hs.604293;Hs.601380 | MIM_ID=
86
+ 17 58011552 T/C 1 15 0 T F214S C RPS6KB1 NA tTt/tCt novel missense_variant ENST00000443572.2:c.641T>C ENSP00000441993.1:p.Phe214Ser 1 probably damaging 0 deleterious 155 NA NA NA NA ENSG00000108443 ENST00000443572 ENSP00000441993 protein_coding 17_55366334 REFSEQ_P= | UNIPROT= | REFSEQ_T= | GENE_DESC=ribosomal protein S6 kinase, 70kDa, polypeptide 1 [Source:HGNC Symbol;Acc:10436] | MIM_DESC= | UNIGENE=Hs.706493;Hs.613833;Hs.568211;Hs.463642;Hs.604293;Hs.601380 | MIM_ID=
87
+ 17 58011552 T/C 1 15 0 T F184S C RPS6KB1 NA tTt/tCt novel missense_variant ENST00000393021.3:c.551T>C ENSP00000376744.3:p.Phe184Ser 1 probably damaging 0 deleterious 155 NA NA NA NA ENSG00000108443 ENST00000393021 ENSP00000376744 protein_coding 17_55366334 REFSEQ_P= | UNIPROT= | REFSEQ_T= | GENE_DESC=ribosomal protein S6 kinase, 70kDa, polypeptide 1 [Source:HGNC Symbol;Acc:10436] | MIM_DESC= | UNIGENE=Hs.706493;Hs.613833;Hs.568211;Hs.463642;Hs.604293;Hs.601380 | MIM_ID=
88
+ 18 39595462 C/T 1 15 0 C L450F T PIK3C3 CCDS11920 Ctt/Ttt novel missense_variant ENST00000262039.4:c.1348C>T ENSP00000262039.3:p.Leu450Phe 0.003 benign 0.52 tolerated 22 2.460 2.758 NA NA ENSG00000078142 ENST00000262039 ENSP00000262039 protein_coding 18_37849460 REFSEQ_P=NP_002638 | UNIPROT=Q8NEB9 | REFSEQ_T=NM_002647.2 | GENE_DESC=phosphatidylinositol 3-kinase, catalytic subunit type 3 [Source:HGNC Symbol;Acc:8974] | MIM_DESC= | UNIGENE=Hs.656958;Hs.464971 | MIM_ID=
89
+ 18 39595462 C/T 1 15 0 C L387F T PIK3C3 NA Ctt/Ttt novel missense_variant ENST00000398870.3:c.1159C>T ENSP00000381845.2:p.Leu387Phe 0.002 benign 0.7 tolerated 22 2.460 2.758 NA NA ENSG00000078142 ENST00000398870 ENSP00000381845 protein_coding 18_37849460 REFSEQ_P= | UNIPROT= | REFSEQ_T= | GENE_DESC=phosphatidylinositol 3-kinase, catalytic subunit type 3 [Source:HGNC Symbol;Acc:8974] | MIM_DESC= | UNIGENE=Hs.656958;Hs.464971 | MIM_ID=
90
+ 18 45423074 C/T -1 15 0 C W18* T SMAD2 NA tgG/tgA novel stop_gained ENST00000587421.1:c.54G>A ENSP00000468202.1:p.Trp18Ter NA NA NA NA NA 4.420 3.576 NA NA ENSG00000175387 ENST00000587421 ENSP00000468202 protein_coding 18_43677072 REFSEQ_P= | UNIPROT= | REFSEQ_T= | GENE_DESC=SMAD family member 2 [Source:HGNC Symbol;Acc:6768] | MIM_DESC= | UNIGENE=Hs.12253;Hs.705764;Hs.702196;Hs.625113;Hs.629015;Hs.617511;Hs.741342 | MIM_ID=
91
+ 18 45423074 C/T -1 15 0 C W18* T SMAD2 CCDS11934 tgG/tgA novel stop_gained ENST00000402690.2:c.54G>A ENSP00000384449.1:p.Trp18Ter NA NA NA NA NA 4.420 3.576 NA NA ENSG00000175387 ENST00000402690 ENSP00000384449 protein_coding 18_43677072 REFSEQ_P=NP_001003652 | UNIPROT=Q15796 | REFSEQ_T=NM_001003652.3 | GENE_DESC=SMAD family member 2 [Source:HGNC Symbol;Acc:6768] | MIM_DESC= | UNIGENE=Hs.12253;Hs.705764;Hs.702196;Hs.625113;Hs.629015;Hs.617511;Hs.741342 | MIM_ID=
92
+ 18 45423074 C/T -1 15 0 C W18* T SMAD2 NA tgG/tgA novel stop_gained ENST00000585978.1:c.54G>A ENSP00000468732.1:p.Trp18Ter NA NA NA NA NA 4.420 3.576 NA NA ENSG00000175387 ENST00000585978 ENSP00000468732 protein_coding 18_43677072 REFSEQ_P= | UNIPROT= | REFSEQ_T= | GENE_DESC=SMAD family member 2 [Source:HGNC Symbol;Acc:6768] | MIM_DESC= | UNIGENE=Hs.12253;Hs.705764;Hs.702196;Hs.625113;Hs.629015;Hs.617511;Hs.741342 | MIM_ID=
93
+ 18 45423074 C/T -1 15 0 C W18* T SMAD2 CCDS11934 tgG/tgA novel stop_gained ENST00000262160.6:c.54G>A ENSP00000262160.6:p.Trp18Ter NA NA NA NA NA 4.420 3.576 NA NA ENSG00000175387 ENST00000262160 ENSP00000262160 protein_coding 18_43677072 REFSEQ_P=NP_005892 | UNIPROT=Q15796 | REFSEQ_T=NM_005901.5 | GENE_DESC=SMAD family member 2 [Source:HGNC Symbol;Acc:6768] | MIM_DESC= | UNIGENE=Hs.12253;Hs.705764;Hs.702196;Hs.625113;Hs.629015;Hs.617511;Hs.741342 | MIM_ID=
94
+ 18 45423074 C/T -1 15 0 C W18* T SMAD2 NA tgG/tgA novel stop_gained ENST00000586514.1:c.54G>A ENSP00000465355.1:p.Trp18Ter NA NA NA NA NA 4.420 3.576 NA NA ENSG00000175387 ENST00000586514 ENSP00000465355 protein_coding 18_43677072 REFSEQ_P= | UNIPROT= | REFSEQ_T= | GENE_DESC=SMAD family member 2 [Source:HGNC Symbol;Acc:6768] | MIM_DESC= | UNIGENE=Hs.12253;Hs.705764;Hs.702196;Hs.625113;Hs.629015;Hs.617511;Hs.741342 | MIM_ID=
95
+ 18 45423074 C/T -1 15 0 C W18* T SMAD2 NA tgG/tgA novel stop_gained ENST00000591214.1:c.54G>A ENSP00000467075.1:p.Trp18Ter NA NA NA NA NA 4.420 3.576 NA NA ENSG00000175387 ENST00000591214 ENSP00000467075 protein_coding 18_43677072 REFSEQ_P= | UNIPROT= | REFSEQ_T= | GENE_DESC=SMAD family member 2 [Source:HGNC Symbol;Acc:6768] | MIM_DESC= | UNIGENE=Hs.12253;Hs.705764;Hs.702196;Hs.625113;Hs.629015;Hs.617511;Hs.741342 | MIM_ID=
96
+ 18 45423074 C/T -1 15 0 C W18* T SMAD2 NA tgG/tgA novel stop_gained ENST00000356825.4:c.54G>A ENSP00000349282.4:p.Trp18Ter NA NA NA NA NA 4.420 3.576 NA NA ENSG00000175387 ENST00000356825 ENSP00000349282 protein_coding 18_43677072 REFSEQ_P=NP_001129409 | UNIPROT=Q15796 | REFSEQ_T=NM_001135937.2 | GENE_DESC=SMAD family member 2 [Source:HGNC Symbol;Acc:6768] | MIM_DESC= | UNIGENE=Hs.12253;Hs.705764;Hs.702196;Hs.625113;Hs.629015;Hs.617511;Hs.741342 | MIM_ID=
97
+ 18 45423074 C/T -1 15 0 C W18* T SMAD2 NA tgG/tgA novel stop_gained ENST00000589877.1:c.54G>A ENSP00000465971.1:p.Trp18Ter NA NA NA NA NA 4.420 3.576 NA NA ENSG00000175387 ENST00000589877 ENSP00000465971 protein_coding 18_43677072 REFSEQ_P= | UNIPROT= | REFSEQ_T= | GENE_DESC=SMAD family member 2 [Source:HGNC Symbol;Acc:6768] | MIM_DESC= | UNIGENE=Hs.12253;Hs.705764;Hs.702196;Hs.625113;Hs.629015;Hs.617511;Hs.741342 | MIM_ID=
98
+ 18 45423074 C/T -1 15 0 C W18* T SMAD2 NA tgG/tgA novel stop_gained ENST00000586040.1:c.54G>A ENSP00000466193.1:p.Trp18Ter NA NA NA NA NA 4.420 3.576 NA NA ENSG00000175387 ENST00000586040 ENSP00000466193 protein_coding 18_43677072 REFSEQ_P= | UNIPROT=Q15796 | REFSEQ_T= | GENE_DESC=SMAD family member 2 [Source:HGNC Symbol;Acc:6768] | MIM_DESC= | UNIGENE=Hs.12253;Hs.705764;Hs.702196;Hs.625113;Hs.629015;Hs.617511;Hs.741342 | MIM_ID=
99
+ 18 45423074 C/T -1 15 0 C W18* T SMAD2 NA tgG/tgA novel stop_gained ENST00000587269.1:c.54G>A ENSP00000466254.1:p.Trp18Ter NA NA NA NA NA 4.420 3.576 NA NA ENSG00000175387 ENST00000587269 ENSP00000466254 protein_coding 18_43677072 REFSEQ_P= | UNIPROT= | REFSEQ_T= | GENE_DESC=SMAD family member 2 [Source:HGNC Symbol;Acc:6768] | MIM_DESC= | UNIGENE=Hs.12253;Hs.705764;Hs.702196;Hs.625113;Hs.629015;Hs.617511;Hs.741342 | MIM_ID=
100
+ 18 59195357 G/A 1 17 0 G G392D A CDH20 CCDS11977 gGc/gAc novel missense_variant ENST00000538374.1:c.1175G>A ENSP00000442226.1:p.Gly392Asp 0.08 benign 0.18 tolerated 94 1.750 2.105 NA NA ENSG00000101542 ENST00000538374 ENSP00000442226 protein_coding 18_57346337 REFSEQ_P= | UNIPROT=Q9HBT6 | REFSEQ_T= | GENE_DESC=cadherin 20, type 2 [Source:HGNC Symbol;Acc:1760] | MIM_DESC= | UNIGENE=Hs.671510 | MIM_ID=
101
+ 18 59195357 G/A 1 17 0 G G392D A CDH20 CCDS11977 gGc/gAc novel missense_variant ENST00000536675.2:c.1175G>A ENSP00000444767.1:p.Gly392Asp 0.08 benign 0.18 tolerated 94 1.750 2.105 NA NA ENSG00000101542 ENST00000536675 ENSP00000444767 protein_coding 18_57346337 REFSEQ_P=NP_114097 | UNIPROT=Q9HBT6 | REFSEQ_T=NM_031891.2 | GENE_DESC=cadherin 20, type 2 [Source:HGNC Symbol;Acc:1760] | MIM_DESC= | UNIGENE=Hs.671510 | MIM_ID=
102
+ 18 59195357 G/A 1 17 0 G G392D A CDH20 CCDS11977 gGc/gAc novel missense_variant ENST00000262717.4:c.1175G>A ENSP00000262717.3:p.Gly392Asp 0.08 benign 0.18 tolerated 94 1.750 2.105 NA NA ENSG00000101542 ENST00000262717 ENSP00000262717 protein_coding 18_57346337 REFSEQ_P= | UNIPROT=Q9HBT6 | REFSEQ_T= | GENE_DESC=cadherin 20, type 2 [Source:HGNC Symbol;Acc:1760] | MIM_DESC= | UNIGENE=Hs.671510 | MIM_ID=
103
+ 21 38884310 C/T 1 10 0 C H581Y T DYRK1A CCDS13653 Cat/Tat novel missense_variant ENST00000339659.3:c.1741C>T ENSP00000340373.3:p.His581Tyr 0.925 probably damaging 0.1 tolerated 83 4.200 3.286 NA NA ENSG00000157540 ENST00000339659 ENSP00000340373 protein_coding 21_37806180 REFSEQ_P=NP_569120 | UNIPROT=Q13627 | REFSEQ_T=NM_130436.2 | GENE_DESC=dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A [Source:HGNC Symbol;Acc:3091] | MIM_DESC= MENTAL RETARDATION, AUTOSOMAL DOMINANT 7; MRD7 | UNIGENE=Hs.719974;Hs.368240 | MIM_ID=614104
104
+ 21 38884310 C/T 1 10 0 C H362Y T DYRK1A NA Cat/Tat novel missense_variant ENST00000455387.2:c.1084C>T ENSP00000407854.2:p.His362Tyr 0.842 possibly damaging 0.17 tolerated 83 4.200 3.286 NA NA ENSG00000157540 ENST00000455387 ENSP00000407854 protein_coding 21_37806180 REFSEQ_P= | UNIPROT= | REFSEQ_T= | GENE_DESC=dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A [Source:HGNC Symbol;Acc:3091] | MIM_DESC= MENTAL RETARDATION, AUTOSOMAL DOMINANT 7; MRD7 | UNIGENE=Hs.719974;Hs.368240 | MIM_ID=614104
105
+ 21 38884310 C/T 1 10 0 C H590Y T DYRK1A CCDS42925 Cat/Tat novel missense_variant ENST00000398960.2:c.1768C>T ENSP00000381932.2:p.His590Tyr 0.842 possibly damaging 0.3 tolerated 83 4.200 3.286 NA NA ENSG00000157540 ENST00000398960 ENSP00000381932 protein_coding 21_37806180 REFSEQ_P=NP_569122,NP_001387 | UNIPROT=Q13627 | REFSEQ_T=NM_001396.3,NM_130438.2 | GENE_DESC=dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A [Source:HGNC Symbol;Acc:3091] | MIM_DESC= MENTAL RETARDATION, AUTOSOMAL DOMINANT 7; MRD7 | UNIGENE=Hs.719974;Hs.368240 | MIM_ID=614104
106
+ #END
metadata ADDED
@@ -0,0 +1,139 @@
1
+ --- !ruby/object:Gem::Specification
2
+ name: bio-locus
3
+ version: !ruby/object:Gem::Version
4
+ version: 0.0.2
5
+ platform: ruby
6
+ authors:
7
+ - Pjotr Prins
8
+ autorequire:
9
+ bindir: bin
10
+ cert_chain: []
11
+ date: 2014-06-05 00:00:00.000000000 Z
12
+ dependencies:
13
+ - !ruby/object:Gem::Dependency
14
+ name: localmemcache
15
+ requirement: !ruby/object:Gem::Requirement
16
+ requirements:
17
+ - - ">="
18
+ - !ruby/object:Gem::Version
19
+ version: '0'
20
+ type: :runtime
21
+ prerelease: false
22
+ version_requirements: !ruby/object:Gem::Requirement
23
+ requirements:
24
+ - - ">="
25
+ - !ruby/object:Gem::Version
26
+ version: '0'
27
+ - !ruby/object:Gem::Dependency
28
+ name: moneta
29
+ requirement: !ruby/object:Gem::Requirement
30
+ requirements:
31
+ - - ">="
32
+ - !ruby/object:Gem::Version
33
+ version: '0'
34
+ type: :runtime
35
+ prerelease: false
36
+ version_requirements: !ruby/object:Gem::Requirement
37
+ requirements:
38
+ - - ">="
39
+ - !ruby/object:Gem::Version
40
+ version: '0'
41
+ - !ruby/object:Gem::Dependency
42
+ name: cucumber
43
+ requirement: !ruby/object:Gem::Requirement
44
+ requirements:
45
+ - - ">="
46
+ - !ruby/object:Gem::Version
47
+ version: '0'
48
+ type: :development
49
+ prerelease: false
50
+ version_requirements: !ruby/object:Gem::Requirement
51
+ requirements:
52
+ - - ">="
53
+ - !ruby/object:Gem::Version
54
+ version: '0'
55
+ - !ruby/object:Gem::Dependency
56
+ name: jeweler
57
+ requirement: !ruby/object:Gem::Requirement
58
+ requirements:
59
+ - - ">="
60
+ - !ruby/object:Gem::Version
61
+ version: '0'
62
+ type: :development
63
+ prerelease: false
64
+ version_requirements: !ruby/object:Gem::Requirement
65
+ requirements:
66
+ - - ">="
67
+ - !ruby/object:Gem::Version
68
+ version: '0'
69
+ - !ruby/object:Gem::Dependency
70
+ name: bundler
71
+ requirement: !ruby/object:Gem::Requirement
72
+ requirements:
73
+ - - ">="
74
+ - !ruby/object:Gem::Version
75
+ version: '0'
76
+ type: :development
77
+ prerelease: false
78
+ version_requirements: !ruby/object:Gem::Requirement
79
+ requirements:
80
+ - - ">="
81
+ - !ruby/object:Gem::Version
82
+ version: '0'
83
+ description: A tool for fast querying and filtering of genome locations in VCF and
84
+ other formats
85
+ email: pjotr.public01@thebird.nl
86
+ executables:
87
+ - bio-locus
88
+ extensions: []
89
+ extra_rdoc_files:
90
+ - LICENSE.txt
91
+ - README.md
92
+ files:
93
+ - ".document"
94
+ - ".rspec"
95
+ - ".travis.yml"
96
+ - Gemfile
97
+ - LICENSE.txt
98
+ - README.md
99
+ - Rakefile
100
+ - VERSION
101
+ - bin/bio-locus
102
+ - features/bio-locus.feature
103
+ - features/step_definitions/bio-locus_steps.rb
104
+ - features/support/env.rb
105
+ - lib/bio-locus.rb
106
+ - lib/bio-locus/locus.rb
107
+ - lib/bio-locus/match.rb
108
+ - lib/bio-locus/store.rb
109
+ - spec/bio-locus_spec.rb
110
+ - spec/spec_helper.rb
111
+ - test/data/input/dbsnp.vcf
112
+ - test/data/input/multisample.vcf
113
+ - test/data/input/somaticsniper.vcf
114
+ - test/data/input/test.snv1
115
+ homepage: http://github.com/pjotrp/bioruby-locus
116
+ licenses:
117
+ - MIT
118
+ metadata: {}
119
+ post_install_message:
120
+ rdoc_options: []
121
+ require_paths:
122
+ - lib
123
+ required_ruby_version: !ruby/object:Gem::Requirement
124
+ requirements:
125
+ - - ">="
126
+ - !ruby/object:Gem::Version
127
+ version: '0'
128
+ required_rubygems_version: !ruby/object:Gem::Requirement
129
+ requirements:
130
+ - - ">="
131
+ - !ruby/object:Gem::Version
132
+ version: '0'
133
+ requirements: []
134
+ rubyforge_project:
135
+ rubygems_version: 2.0.3
136
+ signing_key:
137
+ specification_version: 4
138
+ summary: Fast storage and comparison of chr+pos(+alt) locations
139
+ test_files: []