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

From Bioinformatikpedia
(→‎Investigate the mutations)
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== Sequence-based mutation analysis ==
  
 
[[Lab Journal - Task 8 (PAH) #Sequence-based mutation analysis |Lab journal]] <br>
  
[[Lab Journal - Task 8 (PAH) #Sequence-based mutation analysis |Lab journal]] <br>
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=== Mutation dataset ===
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== Mutation dataset ==
   
 
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===Analyze SNPs===
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==Analyze SNPs==
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====Ala-259-Val====
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===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
 
*Mutation position: ...
  
*Mutation position: ...
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*MutationTaster: disease causing
  
*MutationTaster: disease causing
   
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====Arg-123-Ile====
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===Arg-123-Ile===
 
*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:
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*MutationTaster: disease causing
  
*MutationTaster: disease causing
   
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====Gln-20-Leu====
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===Gln-20-Leu===
 
*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:
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*MutationTaster: disease causing
  
*MutationTaster: disease causing
   
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====Gly-103-Ser====
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===Gly-103-Ser===
 
*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:
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*MutationTaster: disease causing
  
*MutationTaster: disease causing
   
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====His-64-Asn====
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===His-64-Asn===
 
*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:
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*MutationTaster: disease causing
  
*MutationTaster: disease causing
   
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====Ile-421-Thr====
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===Ile-421-Thr===
 
*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:
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*MutationTaster: disease causing
  
*MutationTaster: disease causing
   
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====Lys-341-Thr====
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===Lys-341-Thr===
 
*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:
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*MutationTaster: disease causing
  
*MutationTaster: disease causing
   
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====Phe-392-Ser====
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===Phe-392-Ser===
 
*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:
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*MutationTaster: disease causing
  
*MutationTaster: disease causing
   
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====Pro-416-Gln====
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===Pro-416-Gln===
 
*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:
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*MutationTaster: disease causing
  
*MutationTaster: disease causing
   
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====Thr-266-Ala====
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===Thr-266-Ala===
 
*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:
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*MutationTaster: disease causing
  
*MutationTaster: disease causing
   
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=== Prediction ===
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== Prediction ==
   
 
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Revision as of 14:26, 27 June 2013

Summary

...

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

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/>

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