ASPA Sequence Based Mutation Analysis
Contents
Mutations
CM994594
Mutation: Tyr to Cys at position 231; we got it from dbSNP.
Tyrosine is an highly hydrophobic amino acid due to a benzene ring in its side chain. It occupies considerably more space than the thiol group that cysteine contains. What is more, they are quite hydrophilic and do form hydrogen bonds, both of which is not true of the benzene side chain of tyrosine.
This mutation is very common among Ashkenazi jews and causes Canavan's Disease.
CM940124
Mutation: Ala to Glu at position 305; we got it from dbSNP.
Alanine has a single carbon atom in its side chain, making it hydrophobic and very small. Glutamic acid is an entirely different animal, with a total of three carbon atoms in its side chain, the last of which being part of a carbon acid group. This makes it highly hydrophilic and also leads to a negative charge in the carboxyl group at physiological pH values.
This mutation is very common among Ashkenazi jews and causes Canavan's Disease.
RS104894553
Mutation: Arg to His at position 71; we got it from HGMD.
Arginine is hydrophilic, quite large, with a long side chain and three nitrogen atoms at the end, the chemistry of which gives it a positive charge at physiological pHs. Substituting it by Histidine takes away the charge and substitutes the outmost carbon atom and all of the nitrogen-containing groups with an imidazole group. This leads to a slight decrease in hydrophobicity and not much else.
This mutation is the most common disease-causing mutation among non-jews.
RS104894551
Mutation: Glu to Gly at position 24; we got it from HGMD.
Glutamic acid contains a carboxyl group and carries a negative charge at physiological pHs. Glycine doesn't have anything in the way of a proper side chain, with a hydrogen atom taking its place instead. While glutamic acid is quite hydrophilic, glycine has the chemical properties of the amino acid backbone, which is fairly aliphatic.
RS104894548
Mutation: Cys to Arg at position 152; we got it from HGMD.
Cysteine contains a thiol group, which is hydrophilic and forms hydrogen bridges; Arginine is negatively charged at physiological pHs and hydrophilic and occupies much more space than cysteine.
RS80099330
Mutation: Met to Thr at position 82; we got it from HGMD.
Methionine is a hydrophobic amino acid; Threonine, by contrast, contains an hydroxyl group in the middle of its side chain, which makes it hydrophilic and polar.
CM063847
Mutation: Thr to Ile at position 166; we got it from dbSNP.
The hydrophilic and polar threonine structurally differs not very much from Isoleucine; for the hydroxyl group, a C atom is substituted, and the side chain elongated by another C.
CM990193
Mutation: Pro to His at position 183; we got it from dbSNP.
Proline is hydrophobic and contains a hetero-pentacyclus with one thiol group. Histidin contains such a cyclus, too, but with another nitrogen atom. It carries a positive charge and is hydrophilic.
CM990195
Mutation: Met to Arg at position 195; we got it from dbSNP.
Methionine is hydrophobic; Arginine is positively charged and hydrophilic and more spacious than methionine.
CM055097
Mutation: Lys to Glu at position 213; we got it from dbSNP.
Lysine contains a positively charged nitrogen atom part of an ammonium group; Glutamic acid carries a negative charge on a carboxyl group. Both are hydrophilic and of comparable size.
PSSM
Mutated / Wildtype
A R N D C Q E G H I L K M F P S T W Y V A R N D C Q E G H I L K M F P S T W Y V
24 E -4 -3 -3 -1 -7 0 8 -5 -3 -6 -6 -2 -5 -6 -4 -3 -4 -6 -5 -6 0 0 0 0 0 1 99 0 0 0 0 0 0 0 0 0 0 0 0 0 2.24 1.67
71 R -4 8 -3 -2 -6 -2 -3 -5 -1 -5 -4 -1 1 -5 -5 -3 -4 -5 -4 -5 0 88 0 3 0 0 0 0 1 0 0 0 5 0 0 0 0 0 0 0 1.96 1.46
82 M 1 -2 1 2 -1 0 -1 1 0 -1 -2 -1 2 -3 1 -1 2 -3 -2 -1 10 2 6 10 1 4 4 12 3 4 4 3 5 1 6 5 14 0 2 5 0.15 1.53
152 C -2 -3 -1 1 3 -2 -2 -3 -2 3 -1 -4 2 -2 -2 -3 -2 -5 -1 5 2 2 3 8 6 2 2 2 1 16 3 1 4 1 3 2 2 0 2 39 0.64 2.02
166 T 2 -2 -1 -1 -2 -2 -1 -1 -1 -3 -2 -4 -2 3 -2 2 3 1 3 -1 15 2 2 3 1 1 5 5 1 1 4 1 1 12 2 15 16 2 10 3 0.34 2.09
183 P 0 -1 0 -1 1 0 -1 1 0 -4 -1 -1 0 -1 4 0 -1 4 0 -2 9 3 4 4 3 4 3 12 3 0 6 4 3 3 17 6 3 6 3 3 0.26 1.80
195 M 1 -1 -4 -1 2 -1 -1 1 1 1 0 -4 3 1 -5 -1 2 -5 0 1 12 3 0 3 5 3 3 9 4 9 7 0 9 5 0 4 11 0 4 8 0.21 1.85
213 K -1 1 0 2 1 0 0 -1 1 -1 -1 0 1 0 1 -1 0 -5 0 -1 6 7 4 10 3 5 5 4 3 4 8 7 3 4 8 5 6 0 3 5 0.07 2.08
231 Y 0 0 -4 -4 -2 -2 -2 -3 -4 -1 0 2 1 2 -4 -1 -2 6 4 -1 10 6 0 1 1 1 3 2 0 3 8 14 4 8 1 4 2 13 15 5 0.52 1.95
305 A 3 -4 -5 -5 2 -4 -4 -4 -5 1 2 -4 -2 0 -4 -2 -3 -5 -3 5 24 0 0 0 4 0 0 0 0 7 17 0 0 3 0 3 0 0 0 41 0.71 1.09
Secondary Structure
ASPA: MTSCHIAEEHIQKVAIFGGTHGNELTGVFLVKHWLENGAEIQRTGLEVKPFITNPRAVKKCTRYID
MUT: MTSCHIAEEHIQKVAIFGGTHGNGLTGVFLVKHWLENGAEIQRTGLEVKPFITNPRAVKKCTRYID
SS: ------------EEEEEEEE------HHHHHHHHHH---------EEEEEEEE-HHHHHH-----H
ASPA: CDLNRIFDLENLGKKMSEDLPYEVRRAQEINHLFGPKDSEDSYDIIFDLHNTTSNMGCTLILEDSR
MUT: CDLNHIFDLENLGKKTSEDLPYEVRRAQEINHLFGPKDSEDSYDIIFDLHNTTSNMGCTLILEDSR
SS: ---------------------HHHHHHHHHHHHHH-------EEEEEE-----------EEEE---
ASPA: NNFLIQMFHYIKTSLAPLPCYVYLIEHPSLKYATTRSIAKYPVGIEVGPQPQGVLRADILDQMRKM
MUT: NNFLIQMFHYIKTSLAPLPRYVYLIEHPSLKYAITRSIAKYPVGIEVGPQHQGVLRADILDQRRKM
SS: -HHHHHHHHHHHH------EEEEEE---------HHEE----EEEEE---------HHHHHHHHHH
ASPA: IKHALDFIHHFNEGKEFPPCAIEVYKIIEKVDYPRDENGEIAAIIHPNLQDQDWKPLHPGDPMFLT
MUT: IKHALDFIHHFNEGEEFPPCAIEVYKIIEKVDCPRDENGEIAAIIHPNLQDQDWKPLHPGDPMFLT
SS: HHHHHHHHHHH----------EEEEEEEEEE----------EEEE----------------HHE--
ASPA: LDGKTIPLGGDCTVYPVFVNEAAYYEKKEAFAKTTKLTLNAKSIRCCLH
MUT: LDGKTIPLGGDCTVYPVFVNEEAYYEKKEAFAKTTKLTLNAKSIRCCLH
SS: ----EEEE----EEEEEEE-----HHH-HHHHHHHHEEE-----EEEE-
Multiple Sequence Alignment
We calculated our MSA using T-Coffee
Table of Results
| Mutation | Pos. | Blosum Score | Worst? | PAM250 Score | Worst? | PAM1 Score | Worst? | PSSP Mutated | Wildtype | MSA Mutated | Wildtype | Polyphen Prediction | Score | Sift Prediction | Score | Median Conservation | SNAP Prediction | Reliability | Exp. Accuracy |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Tyr->Cys | 231 | -2 | no | -0.5 | no | 3 | no | -2 | 15 | 0.0% | 73.7% | damaging | 1.0 | affect | 0.00 | 3.02 | Non-neutral | 5 | 87% |
| Ala->Glu | 305 | -1 | no | 0 | no | 17 | no | -4 | 3 | 0.0% | 68.8% | damaging | 1.0 | affect | 0.02 | 3.14 | Non-neutral | 3 | 78% |
| Arg->His | 71 | 0 | no | 0.6 | no | 8 | no | -1 | 8 | 0.0% | 100.0% | damaging | 1.0 | affect | 0.01 | 3.02 | Non-neutral | 6 | 93% |
| Glu->Gly | 24 | -2 | no | -0.8 | no | 7 | no | -5 | 8 | 0.0% | 100.0% | damaging | 1.0 | affect | 0.00 | 3.02 | Non-neutral | 7 | 96% |
| Cys->Arg | 152 | -3 | yes | -2.2 | yes | 1 | no | -3 | 3 | 0.0% | 100.0% | damaging | 0.999 | affect | 0.01 | 3.07 | Non-neutral | 6 | 93% |
| Met->Thr | 82 | -1 | no | -0.6 | no | 6 | no | 14 | 2 | 0.0% | 57.9% | benign | 0.0 | tolerated | 0.16 | 3.02 | Non-neutral | 0 | 58% |
| Thr->Ile | 166 | -1 | no | -0.6 | no | 7 | no | 1 | 16 | 0.0% | 73.7% | damaging | 1.0 | affect | 0.04 | 3.07 | Non-neutral | 2 | 70% |
| Pro->His | 183 | -2 | no | -1.1 | no | 3 | no | 0 | 4 | 5.3% | 94.7% | damaging | 1.0 | affect | 0.00 | 3.07 | Non-neutral | 6 | 93% |
| Met->Arg | 195 | -1 | no | -1.7 | no | 4 | no | -1 | 3 | 0.0% | 94.7% | damaging | 0.991 | affect | 0.03 | 3.04 | Non-neutral | 5 | 87% |
| Lys->Glu | 213 | 1 | no | 1.2 | no | 4 | no | 0 | 0 | 0.0% | 73.7% | benign | 0.014 | tolerated | 0.83 | 3.02 | Neutral | 3 | 78% |
