Difference between revisions of "Seq.-based mut. analysis HEXA"

From Bioinformatikpedia
(Mutations)
(Mutations)
Line 6: Line 6:
 
|mutation codon
 
|mutation codon
 
|mutation triplet
 
|mutation triplet
|aa propensity
 
|consequences
 
 
|-
 
|-
 
|rs121907979
 
|rs121907979
Line 13: Line 11:
 
|Leu -> Arg
 
|Leu -> Arg
 
|CTT -> CGT
 
|CTT -> CGT
|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.
 
 
|-
 
|-
 
|rs11551324
 
|rs11551324
Line 20: Line 16:
 
|Thr -> Thr
 
|Thr -> Thr
 
|ACC -> ACT
 
|ACC -> ACT
  +
|-
  +
|rs61731240
  +
|179
  +
|His -> Asp
  +
|CAT -> GAT
  +
|-
  +
|rs121907974
  +
|211
  +
|Phe -> Ser
  +
|TTC -> TCC
  +
  +
|-
  +
|rs1054374
  +
|293
  +
|Ser -> Ile
  +
|AGT -> ATT
  +
|-
  +
|rs28942072
  +
|324
  +
|Val -> Val
  +
|GTT -> GTA
  +
|-
  +
|rs121907967
  +
|329
  +
|Trp -> TER
  +
|TGG -> TAG
  +
|-
  +
|rs121907982
  +
|436
  +
|Ile -> Val
  +
|ATA -> GTA
  +
|-
  +
|rs121907968
  +
|485
  +
|Trp -> Arg
  +
|gTGG -> CGG
  +
|-
  +
|rs4777502
  +
|506
  +
|Glu -> Glu
  +
|GAG -> GAA
  +
|-
  +
|}
  +
  +
== pysicochemical properities ==
  +
  +
{| border="1" style="text-align:center; border-spacing:0;"
  +
|SNP-id
  +
|mutation codon
  +
|aa propensity
  +
|consequences
  +
|-
  +
|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.
  +
|-
  +
|rs11551324
  +
|Thr -> Thr
 
|polar, small, hydrophilic, neutral -> polar, small, hydrophilic, neutral
 
|polar, small, hydrophilic, neutral -> polar, small, hydrophilic, neutral
 
|no consequences -> silent mutation
 
|no consequences -> silent mutation
 
|-
 
|-
 
|rs61731240
 
|rs61731240
|179
 
 
|His -> Asp
 
|His -> Asp
|CAT -> GAT
 
 
|aromatic, positive charged, polar, hydrophilic -> negative charged, small, polar, hydrophilic
 
|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.
 
|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
 
|rs121907974
|211
 
 
|Phe -> Ser
 
|Phe -> Ser
|TTC -> TCC
 
 
|aromatic, hydrophobic, neutral -> polar, tiny, hydrophilic, neutral
 
|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.
 
|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.
 
|-
 
|-
 
|rs1054374
 
|rs1054374
|293
 
 
|Ser -> Ile
 
|Ser -> Ile
|AGT -> ATT
 
 
|polar, tiny, hydrophilic, neutral -> aliphatic, hydrophobic, neutral
 
|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.
 
|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.
 
|-
 
|-
 
|rs28942072
 
|rs28942072
|324
 
 
|Val -> Val
 
|Val -> Val
|GTT -> GTA
 
 
|aliphatic, hydrophobic, neutral -> aliphatic, hydrophobic, neutral
 
|aliphatic, hydrophobic, neutral -> aliphatic, hydrophobic, neutral
 
|no consequences -> silent mutation
 
|no consequences -> silent mutation
 
|-
 
|-
 
|rs121907967
 
|rs121907967
|329
 
 
|Trp -> TER
 
|Trp -> TER
|TGG -> TAG
 
 
|aromatic, polar, hydrophobic -> 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.
 
|By this change, the protein is not complete, therefore it is not possible for the protein to fold and to function.
 
|-
 
|-
 
|rs121907982
 
|rs121907982
|436
 
 
|Ile -> Val
 
|Ile -> Val
|ATA -> GTA
 
 
|aliphatic, hydrophobic, neutral -> aliphatic, hydrophobic, neutral
 
|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.
 
|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
 
|rs121907968
|485
 
 
|Trp -> Arg
 
|Trp -> Arg
|gTGG -> CGG
 
 
|aromatic, polar, hydrophobic, neutral -> positive charged, polar, hydrophilic
 
|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.
 
|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.
 
|-
 
|-
 
|rs4777502
 
|rs4777502
|506
 
 
|Glu -> Glu
 
|Glu -> Glu
|GAG -> GAA
 
 
|negative charged, polar, hydrophilic -> negative charged, polar, hydrophilic
 
|negative charged, polar, hydrophilic -> negative charged, polar, hydrophilic
 
|no consequences -> silent mutation
 
|no consequences -> silent mutation

Revision as of 15:20, 21 June 2011

Mutations

SNP-id codon number mutation codon mutation triplet
rs121907979 39 Leu -> Arg CTT -> CGT
rs11551324 109 Thr -> Thr ACC -> ACT
rs61731240 179 His -> Asp CAT -> GAT
rs121907974 211 Phe -> Ser TTC -> TCC
rs1054374 293 Ser -> Ile AGT -> ATT
rs28942072 324 Val -> Val GTT -> GTA
rs121907967 329 Trp -> TER TGG -> TAG
rs121907982 436 Ile -> Val ATA -> GTA
rs121907968 485 Trp -> Arg gTGG -> CGG
rs4777502 506 Glu -> Glu GAG -> GAA

pysicochemical properities

SNP-id mutation codon aa propensity consequences
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.
rs11551324 Thr -> Thr polar, small, hydrophilic, neutral -> polar, small, hydrophilic, neutral no consequences -> silent mutation
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.
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.
rs28942072 Val -> Val aliphatic, hydrophobic, neutral -> aliphatic, hydrophobic, neutral no consequences -> silent mutation
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.
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.
rs4777502 Glu -> Glu negative charged, polar, hydrophilic -> negative charged, polar, hydrophilic no consequences -> silent mutation