Difference between revisions of "Seq.-based mut. analysis HEXA"
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| − | == Mutations == |
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| − | |||
| − | {| border="1" style="text-align:center; border-spacing:0;" |
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| − | |SNP-id |
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| − | |codon number |
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| − | |mutation codon |
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| − | |mutation triplet |
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| − | |- |
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| − | |rs121907979 |
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| − | |39 |
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| − | |Leu -> Arg |
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| − | |CTT -> CGT |
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| − | |- |
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| − | |rs11551324 |
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| − | |109 |
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| − | |Thr -> Thr |
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| − | |ACC -> ACT |
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| − | |- |
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| − | |rs61731240 |
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| − | |179 |
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| − | |His -> Asp |
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| − | |CAT -> GAT |
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| − | |- |
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| − | |rs121907974 |
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| − | |211 |
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| − | |Phe -> Ser |
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| − | |TTC -> TCC |
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| − | |||
| − | |- |
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| − | |rs1054374 |
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| − | |293 |
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| − | |Ser -> Ile |
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| − | |AGT -> ATT |
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| − | |- |
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| − | |rs28942072 |
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| − | |324 |
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| − | |Val -> Val |
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| − | |GTT -> GTA |
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| − | |- |
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| − | |rs121907967 |
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| − | |329 |
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| − | |Trp -> TER |
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| − | |TGG -> TAG |
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| − | |- |
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| − | |rs121907982 |
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| − | |436 |
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| − | |Ile -> Val |
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| − | |ATA -> GTA |
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| − | |- |
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| − | |rs121907968 |
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| − | |485 |
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| − | |Trp -> Arg |
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| − | |gTGG -> CGG |
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| − | |- |
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| − | |rs4777502 |
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| − | |506 |
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| − | |Glu -> Glu |
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| − | |GAG -> GAA |
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| − | |- |
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| − | |} |
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| − | |||
| − | == pysicochemical properities == |
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| − | |||
| − | {| border="1" style="text-align:center; border-spacing:0;" |
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| − | |SNP-id |
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| − | |mutation codon |
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| − | |aa propensity |
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| − | |consequences |
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| − | |- |
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| − | |rs121907979 |
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| − | |Leu -> Arg |
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| − | |aliphatic, hydrophobic, neutral -> positive charged, polar, hydrophilic |
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| − | |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. |
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| − | |- |
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| − | |rs11551324 |
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| − | |Thr -> Thr |
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| − | |polar, small, hydrophilic, neutral -> polar, small, hydrophilic, neutral |
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| − | |no consequences -> silent mutation |
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| − | |- |
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| − | |rs61731240 |
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| − | |His -> Asp |
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| − | |aromatic, positive charged, polar, hydrophilic -> negative charged, small, polar, hydrophilic |
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| − | |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. |
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| − | |- |
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| − | |rs121907974 |
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| − | |Phe -> Ser |
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| − | |aromatic, hydrophobic, neutral -> polar, tiny, hydrophilic, neutral |
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| − | |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. |
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| − | |- |
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| − | |rs1054374 |
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| − | |Ser -> Ile |
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| − | |polar, tiny, hydrophilic, neutral -> aliphatic, hydrophobic, neutral |
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| − | |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. |
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| − | |- |
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| − | |rs28942072 |
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| − | |Val -> Val |
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| − | |aliphatic, hydrophobic, neutral -> aliphatic, hydrophobic, neutral |
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| − | |no consequences -> silent mutation |
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| − | |- |
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| − | |rs121907967 |
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| − | |Trp -> TER |
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| − | |aromatic, polar, hydrophobic -> TER |
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| − | |By this change, the protein is not complete, therefore it is not possible for the protein to fold and to function. |
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| − | |- |
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| − | |rs121907982 |
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| − | |Ile -> Val |
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| − | |aliphatic, hydrophobic, neutral -> aliphatic, hydrophobic, neutral |
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| − | |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. |
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| − | |- |
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| − | |rs121907968 |
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| − | |Trp -> Arg |
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| − | |aromatic, polar, hydrophobic, neutral -> positive charged, polar, hydrophilic |
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| − | |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. |
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| − | |- |
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| − | |rs4777502 |
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| − | |Glu -> Glu |
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| − | |negative charged, polar, hydrophilic -> negative charged, polar, hydrophilic |
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| − | |no consequences -> silent mutation |
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| − | |- |
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| − | |} |
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| − | |||
| − | == Visualisation of the mutations == |
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| − | |||
| − | |||
| − | {| border="1" style="text-align:center; border-spacing:0;" |
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| − | |SNP-id |
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| − | |mutation codon |
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| − | |picture original aa |
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| − | |picture mutated aa |
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| − | |combined picture |
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| − | |- |
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| − | |rs121907979 |
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| − | |Leu -> Arg |
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| − | |[[Image:L39.png|thumb|150px|Amino acid Leucine]] |
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| − | |[[Image:39R.png|thumb|150px|Amino acid Arginine]] |
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| − | |[[Image:L39R.png|thumb|150px|Picture which visualize the mutation]] |
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| − | |- |
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| − | |rs11551324 |
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| − | |Thr -> Thr |
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| − | | |
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| − | |[[Image:T109T.png|thumb|150px|Visualisation of the silent mutation]] |
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| − | | |
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| − | |- |
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| − | |rs61731240 |
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| − | |His -> Asp |
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| − | |[[Image:H179.png|thumb|150px|Amino acid Histidine]] |
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| − | |[[Image:179D.png|thumb|150px|Amino acid Aspartate]] |
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| − | |[[Image:H179D.png|thumb|150px|Picture which visualize the mutation]] |
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| − | |- |
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| − | |rs121907974 |
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| − | |Phe -> Ser |
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| − | |[[Image:F211.png|thumb|150px|Amino acid Phenylalanine]] |
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| − | |[[Image:211S.png|thumb|150px|Amino acid Serine]] |
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| − | |[[Image:F211S.png|thumb|150px|Picture which visualize the mutation]] |
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| − | |- |
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| − | |rs1054374 |
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| − | |Ser -> Ile |
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| − | |[[Image:S293.png|thumb|150px|Amino acid Serine]] |
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| − | |[[Image:293I.png|thumb|150px|Amino acid Iseleucine]] |
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| − | |[[Image:S293I.png|thumb|150px|Picture which visualize the mutation]] |
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| − | |- |
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| − | |rs28942072 |
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| − | |Val -> Val |
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| − | | |
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| − | |[[Image:V324V.png|thumb|150px|Visualization of the silent mutation]] |
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| − | | |
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| − | |- |
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| − | |rs121907967 |
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| − | |Trp -> TER |
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| − | |[[Image:W329.png|thumb|150px|Amino acid Tryptophan]] |
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| − | | |
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| − | |[[Image:L39R.png|thumb|150px|Visualization of the mutated protein]] |
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| − | |- |
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| − | |rs121907982 |
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| − | |Ile -> Val |
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| − | |[[Image:I436.png|thumb|150px|Amino acid Iseleucine]] |
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| − | |[[Image:436V.png|thumb|150px|Amino acid Valin]] |
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| − | |[[Image:I436V.png|thumb|150px|Picture which visualize the mutation]] |
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| − | |- |
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| − | |rs121907968 |
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| − | |Trp -> Arg |
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| − | |[[Image:W485.png|thumb|150px|Amino acid Tryptophan]] |
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| − | |[[Image:485R.png|thumb|150px|Amino acid Arginine]] |
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| − | |[[Image:W485R.png|thumb|150px|Picture which visualize the mutation]] |
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| − | |- |
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| − | |rs4777502 |
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| − | |Glu -> Glu |
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| − | | |
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| − | |[[Image:E506E.png|thumb|150px|Visualization of the silent mutation]] |
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| − | | |
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| − | |- |
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| − | |} |
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