Sequence-based mutation analysis (Phenylketonuria)

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
H2Q6R0	G3S964	G1R3M2	G7PJC2	F7HMW9	F7I717	F7BKF9
F6XY00	E2R366	G1T8B6	H2NIF5	M3YKN3	M9P0Q7	H0WTI6
M3W9R1	G3TIW0	G1LIM6	Q2KIH7	G1P4I7	P16331	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 a homologue sequence in canis familiaris

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/>