Difference between revisions of "Sequence-based mutation analysis (Phenylketonuria)"
From Bioinformatikpedia
(→Analyze SNPs) |
(→Analyze SNPs) |
||
| Line 33: | Line 33: | ||
==Analyze SNPs== |
==Analyze SNPs== |
||
| − | [[Lab Journal - Task 8 (PAH) # |
+ | [[Lab Journal - Task 8 (PAH) #Analyze SNPs |Lab journal]] <br> |
===Ala-259-Val=== |
===Ala-259-Val=== |
||
*Amino acid properties: alanine is small, non-polar, neutral and hydrophobic - valine is small, aliphatic, non-polar, neutral and hydrophobic |
*Amino acid properties: alanine is small, non-polar, neutral and hydrophobic - valine is small, aliphatic, non-polar, neutral and hydrophobic |
||
Revision as of 14:27, 27 June 2013
Contents
Summary
...
Mutation dataset
| SNPs | ||
|---|---|---|
| AA - three letter | AA - one letter | Nucleotides |
| Ala259Val | A259V | C776T |
| Arg123Ile | R123I | G368T |
| Gln20Leu | Q20L | A59T |
| Gly103Ser | G103S | G307A |
| His64Asn | H64N | C190A |
| Ile421Thr | I421T | T1262C |
| Lys341Thr | K341T | A1022C |
| Phe392Ser | F392S | T1175C |
| Pro416Gln | P416Q | C1247A |
| Thr266Ala | T266A | A796C |
Analyze SNPs
Ala-259-Val
- Amino acid properties: alanine is small, non-polar, neutral and hydrophobic - valine is small, aliphatic, non-polar, neutral and hydrophobic
- Mutation position: ...
- Structure: HELIX
- Substitution Matrices: middle ranged value -> neutral substitution
- PSSM: ...
- Mammalian homologs: ...
- SIFT: TOLERATED with a score of 0.16
- PolyPhen2: probably damaging
- SNAP:
- MutationTaster: disease causing
Arg-123-Ile
- Amino acid properties: arginine is positively charged, hydrophilic and polar - isoleucine is aliphatic, neutral, non-polar and hydrophobic
- Mutation position:
- Substitution Matrices: low value -> bad substitution
- Structure: LOOP
- PSSM:
- Mammalian homologs:
- SIFT: AFFECT PROTEIN FUNCTION with a score of 0.00
- PolyPhen2: possibly damaging
- SNAP:
- MutationTaster: disease causing
Gln-20-Leu
- Amino acid properties: glutamine is neutral, polar and hydrophilic - leucine is aliphatic, neutral, non-polar and hydrophilic
- Mutation position:
- Substitution Matrices: low value -> bad substitution
- Structure: LOOP
- PSSM:
- Mammalian homologs:
- SIFT: TOLERATED with a score of 0.90
- PolyPhen2: benign
- SNAP:
- MutationTaster: disease causing
Gly-103-Ser
- Amino acid properties: glycine is small, neutral, non-polar and hydrophilic - serine is small, neutral, polar and hydrophilic
- Mutation position:
- Substitution Matrices: middle ranged value -> neutral substitution
- Structure: HELIX
- PSSM:
- Mammalian homologs:
- SIFT: TOLERATED with a score of 0.05
- PolyPhen2: benign
- SNAP:
- MutationTaster: disease causing
His-64-Asn
- Amino acid properties: histidine is positively charged, polar and hydrophobic - asparagine is small, neutral, polar and hydrophilic
- Mutation position:
- Substitution Matrices: middle ranged value -> neutral substitution
- Structure: STRAND
- PSSM:
- Mammalian homologs:
- SIFT: AFFECT PROTEIN FUNCTION with a score of 0.00
- PolyPhen2: probably damaging
- SNAP:
- MutationTaster: disease causing
Ile-421-Thr
- Amino acid properties: isoleucine is aliphatic, neutral, non-polar and hydrophobic - threonine is small, neutral, polar and hydrophobic
- Mutation position:
- Substitution Matrices: low value for Blosum62, middle ranged value for PAM1/250 -> bad or neutral substitution
- Structure: STRAND
- PSSM:
- Mammalian homologs:
- SIFT: AFFECT PROTEIN FUNCTION with a score of 0.00.
- PolyPhen2: probably damaging/possibly damaging
- SNAP:
- MutationTaster: disease causing
Lys-341-Thr
- Amino acid properties: lysine is positively charged, polar and hydrophobic - threonine is small, neutral, polar and hydrophobic
- Mutation position:
- Substitution Matrices: low value for Blosum62, middle ranged value for PAM1/250 -> bad or neutral substitution
- Structure: STRAND
- PSSM:
- Mammalian homologs:
- SIFT: AFFECT PROTEIN FUNCTION with a score of 0.00.
- PolyPhen2: probably damaging
- SNAP:
- MutationTaster: disease causing
Phe-392-Ser
- Amino acid properties: phenylalanine is aromatic, neutral, non-polar and hydrophobic - serine is small, neutral, polar and hydrophilic
- Mutation position:
- Substitution Matrices: low value -> bad substitution
- Structure: HELIX
- PSSM:
- Mammalian homologs:
- SIFT: AFFECT PROTEIN FUNCTION with a score of 0.00.
- PolyPhen2: probably damaging
- SNAP:
- MutationTaster: disease causing
Pro-416-Gln
- Amino acid properties: proline is small, neutral, non-polar and hydrophilic - glutamine is neutral, polar and hydrophilic
- Mutation position:
- Substitution Matrices: low value -> bad substitution
- Structure: LOOP
- PSSM:
- Mammalian homologs:
- SIFT: AFFECT PROTEIN FUNCTION with a score of 0.00.
- PolyPhen2: probably damaging
- SNAP:
- MutationTaster: disease causing
Thr-266-Ala
- Amino acid properties: threonine is small, neutral, polar and hydrophobic - alanine is small, non-polar, neutral and hydrophobic
- Mutation position:
- Substitution Matrices: middle ranged value for Blosum62 and high value for PAM1(TODOPAM250: 11 neutral/high?) -> neutral or good substituion
- Structure: HELIX(ReProf)/LOOP(PsiPred)
- PSSM:
- Mammalian homologs:
- SIFT: AFFECT PROTEIN FUNCTION with a score of 0.00.
- PolyPhen2: probably damaging
- SNAP:
- MutationTaster: disease causing
Prediction
| SNP-Prediction | ||
|---|---|---|
| SNP | Prediction | Validation |
| Ala259Val | ||
| Arg123Ile | ||
| Gln20Leu | ||
| Gly103Ser | ||
| His64Asn | ||
| Ile421Thr | ||
| Lys341Thr | ||
| Phe392Ser | ||
| Pro416Gln | ||
| Thr266Ala | ||
References
<references/>
