Difference between revisions of "Sequence-based mutation analysis (Phenylketonuria)"

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(→‎Investigate the mutations)
(→‎Investigate the mutations)
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*Mutation position: ...
  
*Mutation position: ...
 
*Structure: ...
  
*Structure: ...
−
*Substitution Matrices: for all three matrices this substitution has a score in the middle range.
 +
*Substitution Matrices: middle ranged value -> neutral substitution
 
*PSSM: ...
  
*PSSM: ...
 
*Mammalian homologs: ...
  
*Mammalian homologs: ...
Line 50: Line 50:
 
*Amino acid properties: arginine is positively charged, hydrophilic and polar - isoleucine is aliphatic, neutral, non-polar and hydrophobic
  
*Amino acid properties: arginine is positively charged, hydrophilic and polar - isoleucine is aliphatic, neutral, non-polar and hydrophobic
 
*Mutation position:
  
*Mutation position:
−
*Substitution Matrices:
 +
*Substitution Matrices: low value -> bad substitution
 
*PSSM:
  
*PSSM:
 
*Mammalian homologs:
  
*Mammalian homologs:
Line 61: Line 61:
 
*Amino acid properties: glutamine is neutral, polar and hydrophilic - leucine is aliphatic, neutral, non-polar and hydrophilic
 
*Amino acid properties: glutamine is neutral, polar and hydrophilic - leucine is aliphatic, neutral, non-polar and hydrophilic
 
*Mutation position:
  
*Mutation position:
−
*Substitution Matrices:
 +
*Substitution Matrices: low value -> bad substitution
 
*PSSM:
  
*PSSM:
 
*Mammalian homologs:
  
*Mammalian homologs:
Line 72: Line 72:
 
*Amino acid properties: glycine is small, neutral, non-polar and hydrophilic - serine is small, neutral, polar and hydrophilic
  
*Amino acid properties: glycine is small, neutral, non-polar and hydrophilic - serine is small, neutral, polar and hydrophilic
 
*Mutation position:
  
*Mutation position:
−
*Substitution Matrices:
 +
*Substitution Matrices: middle ranged value -> neutral substitution
 
*PSSM:
  
*PSSM:
 
*Mammalian homologs:
  
*Mammalian homologs:
Line 83: Line 83:
 
*Amino acid properties: histidine is positively charged, polar and hydrophobic - asparagine is small, neutral, polar and hydrophilic
  
*Amino acid properties: histidine is positively charged, polar and hydrophobic - asparagine is small, neutral, polar and hydrophilic
 
*Mutation position:
  
*Mutation position:
−
*Substitution Matrices:
 +
*Substitution Matrices: middle ranged value -> neutral substitution
 
*PSSM:
  
*PSSM:
 
*Mammalian homologs:
  
*Mammalian homologs:
Line 94: Line 94:
 
*Amino acid properties: isoleucine is aliphatic, neutral, non-polar and hydrophobic - threonine is small, neutral, polar and hydrophobic
  
*Amino acid properties: isoleucine is aliphatic, neutral, non-polar and hydrophobic - threonine is small, neutral, polar and hydrophobic
 
*Mutation position:
  
*Mutation position:
−
*Substitution Matrices:
 +
*Substitution Matrices: low value for Blosum62, middle ranged value for PAM1/250 -> bad or neutral substitution
 
*PSSM:
  
*PSSM:
 
*Mammalian homologs:
  
*Mammalian homologs:
Line 105: Line 105:
 
*Amino acid properties: lysine is positively charged, polar and hydrophobic - threonine is small, neutral, polar and hydrophobic
  
*Amino acid properties: lysine is positively charged, polar and hydrophobic - threonine is small, neutral, polar and hydrophobic
 
*Mutation position:
  
*Mutation position:
−
*Substitution Matrices:
 +
*Substitution Matrices: low value for Blosum62, middle ranged value for PAM1/250 -> bad or neutral substitution
 
*PSSM:
  
*PSSM:
 
*Mammalian homologs:
  
*Mammalian homologs:
Line 116: Line 116:
 
*Amino acid properties: phenylalanine is aromatic, neutral, non-polar and hydrophobic - serine is small, neutral, polar and hydrophilic
  
*Amino acid properties: phenylalanine is aromatic, neutral, non-polar and hydrophobic - serine is small, neutral, polar and hydrophilic
 
*Mutation position:
  
*Mutation position:
−
*Substitution Matrices:
 +
*Substitution Matrices: low value -> bad substitution
 
*PSSM:
  
*PSSM:
 
*Mammalian homologs:
  
*Mammalian homologs:
Line 127: Line 127:
 
*Amino acid properties: proline is small, neutral, non-polar and hydrophilic - glutamine is neutral, polar and hydrophilic
  
*Amino acid properties: proline is small, neutral, non-polar and hydrophilic - glutamine is neutral, polar and hydrophilic
 
*Mutation position:
  
*Mutation position:
−
*Substitution Matrices:
 +
*Substitution Matrices: low value -> bad substitution
 
*PSSM:
  
*PSSM:
 
*Mammalian homologs:
  
*Mammalian homologs:
Line 138: Line 138:
 
*Amino acid properties: threonine is small, neutral, polar and hydrophobic - alanine is small, non-polar, neutral and hydrophobic
  
*Amino acid properties: threonine is small, neutral, polar and hydrophobic - alanine is small, non-polar, neutral and hydrophobic
 
*Mutation position:
  
*Mutation position:
  +
*Substitution Matrices: middle ranged value for Blosum62 and high value for PAM1('''TODO'''PAM250: 11 neutral/high?) -> neutral or good substituion
−
*Substitution Matrices:
  
 
*PSSM:
  
*PSSM:
 
*Mammalian homologs:
  
*Mammalian homologs:

Revision as of 12:12, 27 June 2013

Summary

...

Sequence-based mutation analysis

Lab journal

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

Investigate the mutations

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: ...
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • PSSM:
  • Mammalian homologs:
  • SIFT: AFFECT PROTEIN FUNCTION with a score of 0.00.
  • PolyPhen2: probably damaging
  • SNAP:
  • MutationTaster: disease causing

References

<references/>

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