Sequence-based mutation analysis (Phenylketonuria)

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Summary

...

Mutation dataset

Lab journal

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

Lab journal
Looking at the substitution matrices you can see that the substitutions analyzed in this task never have the worst values.
As 2pah begins at position 118 for amino acids 20, 64 and 103 the substitutions cannot be shown with pymol.

Mammalian Homologous Sequences

We used a normal BLAST search on the mammalian database of Uniprot and filter the results per hand for double entries. Altogether we found 22 homologues sequences (<xr id="IDs"/>). <figtable id="IDs">

UniProt-IDs homologue to P00439
http://www.uniprot.org/uniprot/H2Q6R0 H2Q6R0 http://www.uniprot.org/uniprot/G3S964 G3S964 http://www.uniprot.org/uniprot/G1R3M2 G1R3M2 http://www.uniprot.org/uniprot/G7PJC2 G7PJC2 http://www.uniprot.org/uniprot/F7HMW9 F7HMW9 http://www.uniprot.org/uniprot/F7I717 F7I717 http://www.uniprot.org/uniprot/F7BKF9 F7BKF9
http://www.uniprot.org/uniprot/F6XY00 F6XY00 http://www.uniprot.org/uniprot/E2R366 E2R366 http://www.uniprot.org/uniprot/G1T8B6 G1T8B6 http://www.uniprot.org/uniprot/H2NIF5 H2NIF5 http://www.uniprot.org/uniprot/M3YKN3 M3YKN3 http://www.uniprot.org/uniprot/M9P0Q7 M9P0Q7 http://www.uniprot.org/uniprot/H0WTI6 H0WTI6
http://www.uniprot.org/uniprot/M3W9R1 M3W9R1 http://www.uniprot.org/uniprot/G3TIW0 G3TIW0 http://www.uniprot.org/uniprot/G1LIM6 G1LIM6 http://www.uniprot.org/uniprot/Q2KIH7 Q2KIH7 http://www.uniprot.org/uniprot/G1P4I7 G1P4I7 http://www.uniprot.org/uniprot/P16331 P16331 http://www.uniprot.org/uniprot/M9P0Y5 M9P0Y5
UniProt IDs of the 22 mammalian homologues sequences of the PAH protein. The only ID that has a sequence that is not 100% identical to P00439 is marked in green.

</figtable>

For the creation of the multiple alignment we used clustalw. Nevertheless, only F6XY00 has a slightly different sequence. F6XY00 is


Ala-259-Val

<figure id="A259V">

Mutation of alanine to valine at position 259.

</figure>

  • 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: Alanine seems to be highly conserved with a value of 70. Valine has a value of 1.
  • Mammalian homologs: ...
  • SIFT: TOLERATED with a score of 0.16
  • PolyPhen2: probably damaging
  • SNAP:
  • MutationTaster: disease causing

→ prediction = ...


Arg-123-Ile

<figure id="R123I">

Mutation of alanine to valine at position 259.

</figure>

  • 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: Arginine seems to be highly conserved with a value of 49. Isoleucine has a value of 7.
  • Mammalian homologs:
  • SIFT: AFFECT PROTEIN FUNCTION with a score of 0.00
  • PolyPhen2: possibly damaging
  • SNAP:
  • MutationTaster: disease causing

→ prediction = non-neutral

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: seems to be not conserved as aspartic acid has a higher value than glutamine: 17-14. Leucine has a value of 6.
  • Mammalian homologs:
  • SIFT: TOLERATED with a score of 0.90
  • PolyPhen2: benign
  • SNAP:
  • MutationTaster: disease causing

→ prediction = ...

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: Glycine seems to be completely unconserved as every amino acid has the same value 5.
  • Mammalian homologs:
  • SIFT: TOLERATED with a score of 0.05
  • PolyPhen2: benign
  • SNAP:
  • MutationTaster: disease causing

→ prediction = ...

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: Histidine seems to be highly conserved with a value of 58. Asparagine has a value of 2.
  • Mammalian homologs:
  • SIFT: AFFECT PROTEIN FUNCTION with a score of 0.00
  • PolyPhen2: probably damaging
  • SNAP:
  • MutationTaster: disease causing

→ prediction = non-neutral

Ile-421-Thr

<figure id="I421T">

Mutation of alanine to valine at position 259.

</figure>

  • 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: Isoleucine with a value of 32 seems to be not conserved as valine has a value of 41. Threonine has a value of 0.
  • Mammalian homologs:
  • SIFT: AFFECT PROTEIN FUNCTION with a score of 0.00.
  • PolyPhen2: probably damaging/possibly damaging
  • SNAP:
  • MutationTaster: disease causing

→ prediction = non-neutral

Lys-341-Thr

<figure id="K341T">

Mutation of alanine to valine at position 259.

</figure>

  • 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: Lysine seems to be conserved with a value of 39. Threonine has a value of 1.
  • Mammalian homologs:
  • SIFT: AFFECT PROTEIN FUNCTION with a score of 0.00.
  • PolyPhen2: probably damaging
  • SNAP:
  • MutationTaster: disease causing

→ prediction = non-neutral

Phe-392-Ser

<figure id="F392S">

Mutation of alanine to valine at position 259.

</figure>

  • 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: Phenylalanine seems to be highly conserved with a value of 49. Serine has a value of 0.
  • Mammalian homologs:
  • SIFT: AFFECT PROTEIN FUNCTION with a score of 0.00.
  • PolyPhen2: probably damaging
  • SNAP:
  • MutationTaster: disease causing

→ prediction = non-neutral

Pro-416-Gln

<figure id="P416Q">

Mutation of alanine to valine at position 259.

</figure>

  • 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: Proline seems to be highly conserved with a value of 66. Glutamine has a value of 0.
  • Mammalian homologs:
  • SIFT: AFFECT PROTEIN FUNCTION with a score of 0.00.
  • PolyPhen2: probably damaging
  • SNAP:
  • MutationTaster: disease causing

→ prediction = non-neutral

Thr-266-Ala

<figure id="T266A">

Mutation of alanine to valine at position 259.

</figure>

  • 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: Threonine seems to be conserved with a value of 43. Alanine has a value of 29.
  • Mammalian homologs:
  • SIFT: AFFECT PROTEIN FUNCTION with a score of 0.00.
  • PolyPhen2: probably damaging
  • SNAP:
  • MutationTaster: disease causing

→ prediction = non-neutral

Prediction

SNP-Prediction
SNP Prediction Validation
Ala259Val
Arg123Ile non-neutral ?
Gln20Leu
Gly103Ser
His64Asn non-neutral ?
Ile421Thr non-neutral ?
Lys341Thr non-neutral correct
Phe392Ser non-neutral ?
Pro416Gln non-neutral correct
Thr266Ala non-neutral correct

References

<references/>

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