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=== pysicochemical properities === {| border="1" style="text-align:center; border-spacing:0;" |SNP-id |mutation codon |aa propensity |consequences |- |rs4777505 |Asn -> Ser |polar, small, hydrophilic, negatively charged -> polar, tiny, hydrophilic, neutral |Both amino acids are polar and hydrophilic. Ser is tiny, Asn therefore is a small amino acid. The biggest difference between these two amino acid is, that Asn is negatively charged and Ser is neutral. But this is not that big difference and therefore we suggest, that this mutation do not delete the structure and function of the protein. |- |rs121907979 |Leu -> Arg |aliphatic, hydrophobic, neutral -> positive charged, polar, hydrophilic |Leucine is smaller and without a positive charge. Therefore, Arg is too big for the position of Leu, therefore, the change of Leu with Arg has to cause changes in the 3D structure of the protein. Furthermore, Leu is a hydrophobic amino acid, whereas Arg is hydrophilic. This is the complete contrary and therefore we suggest, that the protein will not function any longer. |- |rs61731240 |His -> Asp |aromatic, positive charged, polar, hydrophilic -> negative charged, small, polar, hydrophilic |On the one side, both amino acids are polar, but on the other side, His is positively charged, while Asp is negatively charged, which is an essential difference between these both amino acids. Therefore it is very likely, that this change causes big changes in the structure of the protein and the protein therefore will probably not work any longer. Furthermore, the structure of the two amino acids is very different, because of the aromatic ring of the His. |- |rs121907974 |Phe -> Ser |aromatic, hydrophobic, neutral -> polar, tiny, hydrophilic, neutral |Phe is much bigger than Ser and also contains an aromatic ring. Furthermore, Phe is hydrophobic, whereas Ser is hydrophilic. Because of this, the structure of the protein will change surely and we suggest, that the protein will not work any longer. |- |rs61747114 |Leu -> Phe |aliphatic, hydrophobic, neutral -> aromatic, hydrophobic, neutral |Leu is an aliphatic amino acid, wheras Phe is an aromatic amino acid. This means, that Phe has an aromatic ring in its structure. But both amino acids are relatively big and so it is possible, that the exchange of this amino acids do not change the structure of the protein that much. Therefore, we suggest it is possible, that the protein will work. |- |rs1054374 |Ser -> Ile |polar, tiny, hydrophilic, neutral -> aliphatic, hydrophobic, neutral |Ile is much bigger than Ser and also is branched, because it is an aliphatic amino acid. Therefore the structure of both amino acids is really different and Ile is to big for the position where Ser was. Therefore, there has to be a big change in the 3D structure of the protein and the protein probably will loose its function. |- |rs121907967 |Trp -> TER |aromatic, polar, hydrophobic -> TER |By this change, the protein is not complete, therefore it is not possible for the protein to fold and to function. |- |rs1800430 |Asn -> Asp |polar, small, hydrophilic, negatively charged -> negative charged, small, polar, hydrophilic |Both amino acids have the same properities and therefore we suggest that an exchange of these two amino acids do not destroy the protein structure and function |- |rs121907982 |Ile -> Val |aliphatic, hydrophobic, neutral -> aliphatic, hydrophobic, neutral |In this case, the pysicochemical properties are equal. Furthermore, they almost agree in their size. Therefore, we suggest, that there is no big effect on the 3D structure of the protein and therefore, also no big effect on the protein function. |- |rs121907968 |Trp -> Arg |aromatic, polar, hydrophobic, neutral -> positive charged, polar, hydrophilic |Trp is very big, because of two aromatic rings in its structure. Furthermore, it is hydrophobic, whereas, Arg is a hydrophilic amino acid. Therefore, the changes in the 3D structure might be extreme and delete the function of the protein. |- |} [[http://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Sequence-based_mutation_analysis_HEXA#Summary_page Back to Sequence-based mutation analysis]] === Visualisation of the mutations === {| border="1" style="text-align:center; border-spacing:0;" |SNP-id |mutation codon |picture original aa |picture mutated aa |combined picture |- |rs4777505 |Asn -> Ser |[[Image:N29_2.png|thumb|150px|Amino acid Asparagine]] |[[Image:29S_2.png|thumb|150px|Amino acid Serine]] |[[Image:N29S.png|thumb|150px|Picture which visualize the mutation]] |- |rs121907979 |Leu -> Arg |[[Image:L39.png|thumb|150px|Amino acid Leucine]] |[[Image:39R.png|thumb|150px|Amino acid Arginine]] |[[Image:L39R.png|thumb|150px|Picture which visualize the mutation]] |- |rs61731240 |His -> Asp |[[Image:H179.png|thumb|150px|Amino acid Histidine]] |[[Image:179D.png|thumb|150px|Amino acid Aspartate]] |[[Image:H179D.png|thumb|150px|Picture which visualize the mutation]] |- |rs121907974 |Phe -> Ser |[[Image:F211.png|thumb|150px|Amino acid Phenylalanine]] |[[Image:211S.png|thumb|150px|Amino acid Serine]] |[[Image:F211S.png|thumb|150px|Picture which visualize the mutation]] |- |rs61747114 |Leu -> Phe |[[Image:L248.png|thumb|150px|Amino acid Leucine]] |[[Image:248W.png|thumb|150px|Amino acid Phenylalanine]] |[[Image:L248W.png|thumb|150px|Picture which visualize the mutation]] |- |rs1054374 |Ser -> Ile |[[Image:S293.png|thumb|150px|Amino acid Serine]] |[[Image:293I.png|thumb|150px|Amino acid Isoleucine]] |[[Image:S293I.png|thumb|150px|Picture which visualize the mutation]] |- |rs121907967 |Trp -> TER |[[Image:W329.png|thumb|150px|Amino acid Tryptophan]] | |[[Image:prot_ter.png|thumb|150px|Visualization of the mutated protein]] |- |rs1800430 |Asn -> Asp |[[Image:N399.png|thumb|150px|Amino acid Asparagine]] |[[Image:399D.png|thumb|150px|Amino acid Aspartic acid]] |[[Image:N399D.png|thumb|150px|Picture which visualize the mutation]] |- |rs121907982 |Ile -> Val |[[Image:I436.png|thumb|150px|Amino acid Isoleucine]] |[[Image:436V.png|thumb|150px|Amino acid Valin]] |[[Image:I436V.png|thumb|150px|Picture which visualize the mutation]] |- |rs121907968 |Trp -> Arg |[[Image:W485.png|thumb|150px|Amino acid Tryptophan]] |[[Image:485R.png|thumb|150px|Amino acid Arginine]] |[[Image:W485R.png|thumb|150px|Picture which visualize the mutation]] |- |} [[http://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Sequence-based_mutation_analysis_HEXA#Summary_page Back to Sequence-based mutation analysis]] === Substitutions Matrices === {| border="1" style="text-align:center; border-spacing:0;" |rowspan="2" | SNP-id |rowspan="2" | mutation codon |colspan="3" | PAM 1 |colspan="3" | Pam 250 |colspan="3" | BLOSOUM 62 |- |value aa |most frequent substitution |rarest substitution |value aa |most frequent substitution |rarest substitution |value aa |most frequent substitution |rarest substitution |- |rs4777505 |Asn -> Ser |20 |36 (Asp) |0 (Cys, Met) |5 |7 (Asp) |2 (Cys, Leu, Phe, Trp) |1 |1 (Asp, His, Ser) | -4 (Trp) |- |rs121907979 |Leu -> Arg |1 |22 (Ile) |0 (Asp, Cys) |4 |20 (Met) |2 (Cys) | -2 |0 (Phe) | -4 (Asp, Gly) |- |rs61731240 |His -> Asp |3 |20 (Gln) |0 (Ile, Met) |4 |7 (Gln) |2 (Ala, Cys, Gly, Ile, Leu, Met, Phe, Thr, Trp, Val) | -1 |2 (Tyr) | -3 (Cys, Ile, Leu, Val) |- |rs121907974 |Phe -> Ser |2 |28 (Tyr) |0 (Asp, Cys, Glu, Lys, Pro, Val) |2 |20 (Tyr) |1 (Arg, Asp, Cys, Gln, Glu, Gly, Lys, Pro) | -2 |3 (Tyr) | -4 (Pro) |- |rs61747114 |Leu -> Phe |13 |45 (Met) |0 (Asp, Cys) |13 |20 (Met) |2 (Cys) |0 |2 (Ile, Met) | -4 (Asp, Gly) |- |rs1054374 |Ser -> Ile |2 |38 (Thr) |1 (Leu) |5 |9 (Ala, Gly, Pro, Thr) |3 (Phe) | -2 |1 (Ala, Asn, Thr) | -3 (Trp) |- |rs121907967 |Trp -> TER |X |2 (Arg) |0 (all, except Arg, Phe, Ser, Tyr) |X |2 (Arg) |0 (all, except Arg, His, Leu, Phe, Ser, Tyr) |X |2 (Tyr) | -4 (Asn, Asp, Pro) |- |rs1800430 |Asn -> Asp |36 |36 (Asp) |0 (Cys, Met) |7 |7 (Asp) |2 (Cys, Leu, Phe, Trp) |1 |1 (Asp, His, Ser) | -4 (Trp) |- |rs121907982 |Ile -> Val |33 |33 (Val) |0 (Gly, Pro, Trp) |9 |9 (Val) |1 (Trp) |3 |3 (Val) | -4 (Gly) |- |rs121907968 |Trp -> Arg |2 |2 (Arg) |0 (all, except Arg, Phe, Ser, Tyr) |2 |2 (Arg) |0 (all, except Arg, His, Leu, Phe, Ser, Tyr) | -3 |2 (Tyr) | -4 (Asn, Asp, Pro) |- |} [[http://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Sequence-based_mutation_analysis_HEXA#Summary_page Back to Sequence-based mutation analysis]]

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