Sequence-based mutation analysis HEXA
From Bioinformatikpedia
Contents
Mutations
| SNP-id | codon number | mutation codon | mutation triplet |
| rs4777505 | 29 | Asn -> Ser | AAC -> AGC |
| rs121907979 | 39 | Leu -> Arg | CTT -> CGT |
| rs61731240 | 179 | His -> Asp | CAT -> GAT |
| rs121907974 | 211 | Phe -> Ser | TTC -> TCC |
| rs61747114 | 248 | Leu -> Phe | CTT -> TTT |
| rs1054374 | 293 | Ser -> Ile | AGT -> ATT |
| rs121907967 | 329 | Trp -> TER | TGG -> TAG |
| rs1800430 | 399 | Asn -> Asp | AAC -> GAC |
| rs121907982 | 436 | Ile -> Val | ATA -> GTA |
| rs121907968 | 485 | Trp -> Arg | gTGG -> CGG |
Analysis of the mutations
rs4777505: Asn -> Ser
pysicochemical properities
| Asn | Ser | consequences |
| 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. |
Visualisation of the mutation
| picture original aa | picture mutated aa | combined picture |
Subsitution Matrices values
| PAM 1 | Pam 250 | BLOSOUM 62 | ||||||
| value aa | most frequent substitution | rarest substitution | value aa | most frequent substitution | rarest substitution | value aa | most frequent substitution | rarest substitution |
| 20 | 36 (Asp) | 0 (Cys, Met) | 5 | 7 (Asp) | 2 (Cys, Leu, Phe, Trp) | 1 | 1 (Asp, His, Ser) | -4 (Trp) |
Conservation analysis with multiple alignments
rs121907979: Leu -> Arg
pysicochemical properities
| Leu | Arg | consequences |
| 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. |
Visualisation of the mutation
| picture original aa | picture mutated aa | combined picture |
Subsitution Matrices values
| PAM 1 | Pam 250 | BLOSOUM 62 | ||||||
| value aa | most frequent substitution | rarest substitution | value aa | most frequent substitution | rarest substitution | value aa | most frequent substitution | rarest substitution |
| 1 | 22 (Ile) | 0 (Asp, Cys) | 4 | 20 (Met) | 2 (Cys) | -2 | 0 (Phe) | -4 (Asp, Gly) |
rs61731240: His -> Asp
pysicochemical properities
| His | Asp | consequences |
| 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. |
Visualisation of the mutation
| picture original aa | picture mutated aa | combined picture |
Subsitution Matrices values
| PAM 1 | Pam 250 | BLOSOUM 62 | ||||||
| value aa | most frequent substitution | rarest substitution | value aa | most frequent substitution | rarest substitution | value aa | most frequent substitution | rarest substitution |
| 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
pysicochemical properities
| Phe | Ser | consequences |
| 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. |
Visualisation of the mutation
| picture original aa | picture mutated aa | combined picture |
Subsitution Matrices values
| PAM 1 | Pam 250 | BLOSOUM 62 | ||||||
| value aa | most frequent substitution | rarest substitution | value aa | most frequent substitution | rarest substitution | value aa | most frequent substitution | rarest substitution |
| 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
pysicochemical properities
| Leu | Phe | consequences |
| 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. |
Visualisation of the mutation
| picture original aa | picture mutated aa | combined picture |
Subsitution Matrices values
| PAM 1 | Pam 250 | BLOSOUM 62 | ||||||
| value aa | most frequent substitution | rarest substitution | value aa | most frequent substitution | rarest substitution | value aa | most frequent substitution | rarest substitution |
| 13 | 45 (Met) | 0 (Asp, Cys) | 13 | 20 (Met) | 2 (Cys) | 0 | 2 (Ile, Met) | -4 (Asp, Gly) |
rs1054374: Ser -> Ile
pysicochemical properities
| Ser | Ile | consequences |
| polar, tiny, hydrophilic, neutral | aliphatic, hydrophobic, neutra | 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. |
Visualisation of the mutation
| picture original aa | picture mutated aa | combined picture |
Subsitution Matrices values
| PAM 1 | Pam 250 | BLOSOUM 62 | ||||||
| value aa | most frequent substitution | rarest substitution | value aa | most frequent substitution | rarest substitution | value aa | most frequent substitution | rarest substitution |
| 2 | 38 (Thr) | 1 (Leu) | 5 | 9 (Ala, Gly, Pro, Thr) | 3 (Phe) | -2 | 1 (Ala, Asn, Thr) | -3 (Trp) |
rs121907967: Trp -> TER
pysicochemical properities
| Trp | TER | consequences |
| 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. |
Visualisation of the mutation
| picture original aa | picture mutated aa | combined picture |
Subsitution Matrices values
| PAM 1 | Pam 250 | BLOSOUM 62 | ||||||
| value aa | most frequent substitution | rarest substitution | value aa | most frequent substitution | rarest substitution | value aa | most frequent substitution | rarest substitution |
| 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
pysicochemical properities
| Asn | Asp | consequences |
| polar, small, hydrophilic, negatively charged | polar, small, hydrophilic, negatively charged | 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 |
Visualisation of the mutation
| picture original aa | picture mutated aa | combined picture |
Subsitution Matrices values
| PAM 1 | Pam 250 | BLOSOUM 62 | ||||||
| value aa | most frequent substitution | rarest substitution | value aa | most frequent substitution | rarest substitution | value aa | most frequent substitution | rarest substitution |
| 36 | 36 (Asp) | 0 (Cys, Met) | 7 | 7 (Asp) | 2 (Cys, Leu, Phe, Trp) | 1 | 1 (Asp, His, Ser) | -4 (Trp) |
rs121907982: Ile -> Val
pysicochemical properities
| Ile | Val | consequences |
| aliphatic, hydrophobic, neutra | 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. |
Visualisation of the mutation
| picture original aa | picture mutated aa | combined picture |
Subsitution Matrices values
| PAM 1 | Pam 250 | BLOSOUM 62 | ||||||
| value aa | most frequent substitution | rarest substitution | value aa | most frequent substitution | rarest substitution | value aa | most frequent substitution | rarest substitution |
| 33 | 33 (Val) | 0 (Gly, Pro, Trp) | 9 | 9 (Val) | 1 (Trp) | 3 | 3 (Val) | -4 (Gly) |
rs121907968: Trp -> Arg
pysicochemical properities
| Trp | Arg | consequences |
| 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. |
Visualisation of the mutation
| picture original aa | picture mutated aa | combined picture |
Subsitution Matrices values
| PAM 1 | Pam 250 | BLOSOUM 62 | ||||||
| value aa | most frequent substitution | rarest substitution | value aa | most frequent substitution | rarest substitution | value aa | most frequent substitution | rarest substitution |
| 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) |
Summary page
[Here] you can find all results of the different analysis in one table.
