Difference between revisions of "Lab Journal - Task 7 (PAH)"

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===Mutation Map===
  
===Mutation Map===
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In the table below all 100 SNPs that can be viewed in the mutation map are listed. The second column represent the nucleotide position, the third, which nucleotide is exchanged in which one, the fourth gives the amino acid substitution with codon position and the last column shows the database from which the SNP was taken. We take 50 SNPs of HGMD and 50 SNPs of OMIM and dbSNP. All OMIM SNPs also are found in dbSNP. We only included a few more from dbSNP alone, for which the effect of the SNP is untested in most cases. Except for those few SNPs all others cause PKU according to the databases.
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{|border=1
  
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{|border=1 cellspacing="0" cellpadding="5" style="text-align:center"
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! style="background:#32CD32;" | SNP ID
  +
! style="background:#32CD32;" | Pos. (bp)
  +
! style="background:#32CD32;" | Nucleotides
  +
! style="background:#32CD32;" | Amino acids
  +
! style="background:#32CD32;" | Database
 
|-
  
|-
 
|rs62514891||1||A>G||Met1Val||OMIM/dbSNP
  
|rs62514891||1||A>G||Met1Val||OMIM/dbSNP
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|-
  
|-
 
|CM961070||434||A>T||Asp145Val||HGMD
  
|CM961070||434||A>T||Asp145Val||HGMD
  +
|-
  +
|rs80297647||442||G>A||Gly148Ser||dbSNP,untested
 
|-
  
|-
 
|CM056668||470||G>T||Arg157Ile||HGMD
  
|CM056668||470||G>T||Arg157Ile||HGMD
 
|-
  
|-
 
|rs5030843||473||G>A||Arg158Gln||OMIM/dbSNP
  
|rs5030843||473||G>A||Arg158Gln||OMIM/dbSNP
  +
|-
  +
|rs199475626||493||G>C||Ala165Pro||dbSNP,untested
 
|-
  
|-
 
|CM992371||506||G>A||Arg169His||HGMD
  
|CM992371||506||G>A||Arg169His||HGMD
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|CM011946||508||C>G||His170Asp||HGMD
  
|CM011946||508||C>G||His170Asp||HGMD
 
|-
  
|-
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|rs192592111||516||G>T||Gln172His||dbSNP
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|rs192592111||516||G>T||Gln172His||dbSNP,untested
 
|-
  
|-
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|CM981435||561||G>C||Trp187Cys||HGMD|-
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|CM981435||561||G>C||Trp187Cys||HGMD
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|
  
 
|-
  
|-
 
|CM950887||581||T>C||Leu194Pro||HGMD
  
|CM950887||581||T>C||Leu194Pro||HGMD
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|-
  
|-
 
|CM971131||673||C>A||Pro225Thr||HGMD
  
|CM971131||673||C>A||Pro225Thr||HGMD
  +
|-
  +
|rs62517178||715||G>A||Gly239Ser||dbSNP,untested
 
|-
  
|-
 
|CM034744||716||G>A||Gly239Asp||HGMD
  
|CM034744||716||G>A||Gly239Asp||HGMD
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|CM981442||794||G>A||Cys265Tyr||HGMD
  
|CM981442||794||G>A||Cys265Tyr||HGMD
 
|-
  
|-
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|rs62508752||796||A>C||Thr266Ala||dbSNP
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|rs62508752||796||A>C||Thr266Ala||dbSNP,untested
 
|-
  
|-
 
|CM081725||813||T>G||His271Gln||HGMD
  
|CM081725||813||T>G||His271Gln||HGMD
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|-
  
|-
 
|rs5030851||842||C>T||Pro281Leu||OMIM/dbSNP
  
|rs5030851||842||C>T||Pro281Leu||OMIM/dbSNP
  +
|-
  +
|rs62507327||864||G>C||Leu288Phe||dbSNP,untested
 
|-
  
|-
 
|CM055475||869||A>G||His290Arg||HGMD
  
|CM055475||869||A>G||His290Arg||HGMD
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|-
  
|-
 
|CM010981||1022||A>C||Lys341Thr||HGMD
  
|CM010981||1022||A>C||Lys341Thr||HGMD
  +
|-
  +
|rs62508651||1027||T>G||Tyr343Asp||dbSNP,untested
 
|-
  
|-
 
|CM000550||1031||G>T||Gly344Val||HGMD
  
|CM000550||1031||G>T||Gly344Val||HGMD
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|rs5030856||1169||A>G||Glu390Gly||OMIM/dbSNP
  
|rs5030856||1169||A>G||Glu390Gly||OMIM/dbSNP
 
|-
  
|-
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|rs199475695||1175||T>C||Phe392Ser||dbSNP
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|rs199475695||1175||T>C||Phe392Ser||dbSNP,untested
 
|-
  
|-
 
|CM043319||1184||C>A||Ala395Asp||HGMD
  
|CM043319||1184||C>A||Ala395Asp||HGMD
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|rs62644473||1220||C>T||Pro407Leu||OMIM/dbSNP
  
|rs62644473||1220||C>T||Pro407Leu||OMIM/dbSNP
 
|-
  
|-
−
|rs5030858||1222||C>T||Arg408Trp||dbSNP
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|rs5030858||1222||C>T||Arg408Trp||dbSNP,PKU
 
|-
  
|-
 
|rs5030859||1223||G>A||Arg408Gln||OMIM/dbSNP
  
|rs5030859||1223||G>A||Arg408Gln||OMIM/dbSNP
  +
|-
  +
|rs62644467||1237||C>T||Arg413Cys||dbSNP,untested
 
|-
  
|-
 
|rs79931499||1238||G>C||Arg413Pro||OMIM/dbSNP
  
|rs79931499||1238||G>C||Arg413Pro||OMIM/dbSNP
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|CM920565||1252||A>C||Thr418Pro||HGMD
  
|CM920565||1252||A>C||Thr418Pro||HGMD
 
|-
  
|-
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|rs199475696||1262||T>C||Ile421Thr||dbSNP
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|rs199475696||1262||T>C||Ile421Thr||dbSNP,untested
 
|-
  
|-
 
|CM993961||1271||T>C||Leu424Ser||HGMD
  
|CM993961||1271||T>C||Leu424Ser||HGMD

Latest revision as of 10:38, 6 August 2013

Mutation Map

In the table below all 100 SNPs that can be viewed in the mutation map are listed. The second column represent the nucleotide position, the third, which nucleotide is exchanged in which one, the fourth gives the amino acid substitution with codon position and the last column shows the database from which the SNP was taken. We take 50 SNPs of HGMD and 50 SNPs of OMIM and dbSNP. All OMIM SNPs also are found in dbSNP. We only included a few more from dbSNP alone, for which the effect of the SNP is untested in most cases. Except for those few SNPs all others cause PKU according to the databases.

SNP ID Pos. (bp) Nucleotides Amino acids Database
rs62514891 1 A>G Met1Val OMIM/dbSNP
CM000541 2 T>G Met1Arg HGMD
rs62514893 3 G>A Met1Ile OMIM/dbSNP
CM010947 46 T>C Ser16Pro HGMD
CM000542 59 A>T Gln20Leu HGMD
HM972014 65 C>A Thr22Lys HGMD
rs62642926 117 C>G Phe39Leu OMIM/dbSNP
CM961063 119 C>T Ser40Leu HGMD
rs74603784 136 G>A Gly46Ser OMIM/dbSNP
CM993577 140 C>A Ala47Glu HGMD
rs5030841 143 T>C Leu48Ser OMIM/dbSNP
CM981427 158 G>A Arg53His HGMD
CM024619 181 A>G Asn61Asp HGMD
rs75193786 194 T>C Ile65Thr OMIM/dbSNP
CM981429 208 T>C Ser70Pro HGMD
CM961066 250 G>T Asp84Tyr HGMD
CM981431 281 T>G Ile94Ser HGMD
CM992944 299 A>G His100Arg HGMD
CM045080 307 G>A Gly103Ser HGMD
CM010951 329 C>T Ser110Leu HGMD
rs76296470 331 C>T Arg111Ter OMIM/dbSNP
CM971124 365 C>A Pro122Gln HGMD
rs199475681 368 G>T Arg123Ile dbSNP
CM010952 385 G>T Asp129Tyr HGMD
CM981432 395 C>T Ala132Val HGMD
CM961070 434 A>T Asp145Val HGMD
rs80297647 442 G>A Gly148Ser dbSNP,untested
CM056668 470 G>T Arg157Ile HGMD
rs5030843 473 G>A Arg158Gln OMIM/dbSNP
rs199475626 493 G>C Ala165Pro dbSNP,untested
CM992371 506 G>A Arg169His HGMD
CM011946 508 C>G His170Asp HGMD
rs192592111 516 G>T Gln172His dbSNP,untested
CM981435 561 G>C Trp187Cys HGMD
CM950887 581 T>C Leu194Pro HGMD
CM981438 608 G>A Cys203Tyr HGMD
rs62514927 611 A>G Tyr204Cys OMIM/dbSNP
CM010961 648 C>G Tyr216Term HGMD
rs62514934 662 A>G Glu221Gly OMIM/dbSNP
CM971131 673 C>A Pro225Thr HGMD
rs62517178 715 G>A Gly239Ser dbSNP,untested
CM034744 716 G>A Gly239Asp HGMD
rs5030846 727 C>T Arg243Ter OMIM/dbSNP
rs62508588 728 G>A Arg243Gln OMIM/dbSNP
rs118203923 731 C>T Pro244Leu OMIM/dbSNP
CM920550 731 C>T Pro244Leu HGMD
rs5030847 754 C>T Arg252Trp OMIM/dbSNP
CM920553 763 T>G Leu255Val HGMD
rs62642930 764 T>C Leu255Ser OMIM/dbSNP
rs118203921 776 C>T Ala259Val OMIM/dbSNP
CM910286 776 C>T Ala259Val HGMD
rs5030850 781 C>T Arg261Ter OMIM/dbSNP
rs5030849 782 G>A Arg261Gln OMIM/dbSNP
CM981442 794 G>A Cys265Tyr HGMD
rs62508752 796 A>C Thr266Ala dbSNP,untested
CM081725 813 T>G His271Gln HGMD
rs62514952 814 G>T Gly272Ter OMIM/dbSNP
rs62514953 818 C>T Ser273Phe OMIM/dbSNP
CM034745 827 T>G Met276Arg HGMD
rs78655458 829 T>G Tyr277Asp OMIM/dbSNP
rs62508698 838 G>A Glu280Lys OMIM/dbSNP
CM992948 841 C>T Pro281Ser HGMD
rs5030851 842 C>T Pro281Leu OMIM/dbSNP
rs62507327 864 G>C Leu288Phe dbSNP,untested
CM055475 869 A>G His290Arg HGMD
rs62642933 896 T>G Phe299Cys OMIM/dbSNP
CM015134 922 C>T Leu308Phe HGMD
rs62642936 932 T>C Leu311Pro OMIM/dbSNP
CM024623 940 C>T Pro314Ser HGMD
rs62514959 977 G>A Trp326Ter OMIM/dbSNP
CM990999 981 T>G Phe327Leu HGMD
CM961082 992 T>G Phe331Cys HGMD
CM043317 1007 A>G Gln336Arg HGMD
CM010981 1022 A>C Lys341Thr HGMD
rs62508651 1027 T>G Tyr343Asp dbSNP,untested
CM000550 1031 G>T Gly344Val HGMD
rs62508646 1045 T>C Ser349Pro OMIM/dbSNP
CM981453 1048 T>A Ser350Thr HGMD
rs62516095 1068 C>G Tyr356Ter OMIM/dbSNP
CM101146 1071 C>A Cys357Term HGMD
rs5030854 1076 C>G Ser359Ter OMIM/dbSNP
CM068054 1089 G>T Lys363Asn HGMD
CM010984 1130 A>G Tyr377Cys HGMD
CM950896 1157 A>G Tyr386Cys HGMD
rs62516101 1162 G>A Val388Met OMIM/dbSNP
rs5030856 1169 A>G Glu390Gly OMIM/dbSNP
rs199475695 1175 T>C Phe392Ser dbSNP,untested
CM043319 1184 C>A Ala395Asp HGMD
CM030921 1204 T>C Phe402Leu HGMD
rs62644473 1220 C>T Pro407Leu OMIM/dbSNP
rs5030858 1222 C>T Arg408Trp dbSNP,PKU
rs5030859 1223 G>A Arg408Gln OMIM/dbSNP
rs62644467 1237 C>T Arg413Cys dbSNP,untested
rs79931499 1238 G>C Arg413Pro OMIM/dbSNP
CM101145 1242 C>A Tyr414Term HGMD
CM090791 1247 C>A Pro416Gln HGMD
CM920565 1252 A>C Thr418Pro HGMD
rs199475696 1262 T>C Ile421Thr dbSNP,untested
CM993961 1271 T>C Leu424Ser HGMD
CM010986 1289 T>C Leu430Pro HGMD
CM961086 1340 C>A Ala447Asp HGMD
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