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
Gln172His	Q172H	G516T
Gly103Ser	G103S	G307A
Ile421Thr	I421T	T1262C
Lys341Thr	K341T	A1022C
Phe392Ser	F392S	T1175C
Pro416Gln	P416Q	C1247A
Thr266Ala	T266A	A796C

Analyze SNPs

The complete results of the prediction tools can be found in the 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 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. Like E2R366 F6XY00 is a homologue sequence of the human PAH in canis familiaris. On the positions of our substitutions the sequences are conserved.

Ala-259-Val

<figure id="A259V">

Mutation of alanine to valine at position 259.

</figure>

Properties	alanine is small, non-polar, neutral and hydrophobic
	valine is aliphatic, small, non-polar, neutral and hydrophobic
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.
SIFT	TOLERATED with a score of 0.16
PolyPhen2	probably damaging with a score of 1.000
SNAP	non-neutral, RI = 2
MutationTaster	disease causing
⇒ prediction: neutral/non-neutral???

Arg-123-Ile

<figure id="R123I">

Mutation of alanine to valine at position 259.

</figure>

Properties	arginine is positively charged, polar and hydrophilic
	isoleucine is aliphatic, neutral, non-polar and hydrophobic
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.
SIFT	AFFECT PROTEIN FUNCTION with a score of 0.00
PolyPhen2	possibly damaging with a score of 0.807 / 0.582
SNAP	neutral, RI = 0
MutationTaster	disease causing
⇒ prediction: non-neutral

Gln-20-Leu

Properties	glutamine is neutral, polar and hydrophilic
	leucine is aliphatic, neutral, non-polar and hydrophilic
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.
SIFT	TOLERATED with a score of 0.90
PolyPhen2	benign with a score of 0.000
SNAP	neutral, RI = 0
MutationTaster	disease causing
⇒ prediction: neutral

Gln-172-His

<figure id="Q172H">

Mutation of glutamine to histidine at position 172.

</figure>

Properties	glutamine is neutral, polar and hydrophilic
	histidine is positively charged, polar and hydrophobic
Substitution Matrices	middle ranged → neutral substitution
Structure	LOOP
PSSM	...
SIFT	AFFECT PROTEIN FUNCTION with a score of 0.03.
PolyPhen2	possibly damaging with a score of 0.705 / benign with a score of 0.170
SNAP	neutral, RI = 4
MutationTaster	disease causing
⇒ prediction: neutral

Gly-103-Ser

Properties	glycine is small, neutral, non-polar and hydrophilic
	serine is small, neutral, polar and hydrophilic
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.
SIFT	TOLERATED with a score of 0.05
PolyPhen2	benign with a score of 0.003 / 0.006
SNAP	neutral, RI = 6
MutationTaster	disease causing
⇒ prediction: neutral

Ile-421-Thr

<figure id="I421T">

Mutation of isoleucine to threonine at position 421.

</figure>

Properties	isoleucine is aliphatic, neutral, non-polar and hydrophobic
	threonine is small, neutral, polar and hydrophobic
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.
SIFT	AFFECT PROTEIN FUNCTION with a score of 0.00.
PolyPhen2	possibly damaging with a score of 0.667 / probably damaging with a score of 0.913
SNAP	non-neutral, RI = 2
MutationTaster	disease causing
⇒ prediction: non-neutral

Lys-341-Thr

<figure id="K341T">

Mutation of lysine to threonine at position 341.

</figure>

Properties	lysine is positively charged, polar and hydrophobic
	threonine is small, neutral, polar and hydrophobic
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.
SIFT	AFFECT PROTEIN FUNCTION with a score of 0.00.
PolyPhen2	probably damaging with a score of 1.000 / 0.996
SNAP	non-neutral, RI = 3
MutationTaster	disease causing
⇒ prediction: non-neutral

Phe-392-Ser

<figure id="F392S">

Mutation of phenylalanine to serine at position 392.

</figure>

Properties	phenylalanine is aromatic, neutral, non-polar and hydrophobic
	serine is small, neutral, polar and hydrophilic
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.
SIFT	AFFECT PROTEIN FUNCTION with a score of 0.00.
PolyPhen2	probably damaging with a score of 1.000
SNAP	non-neutral, RI = 1
MutationTaster	disease causing
⇒ prediction: non-neutral

Pro-416-Gln

<figure id="P416Q">

Mutation of proline to glutamine at position 416.

</figure>

Properties	proline is small, neutral, non-polar and hydrophilic
	glutamine is neutral, polar and hydrophilic
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.
SIFT	AFFECT PROTEIN FUNCTION with a score of 0.00.
PolyPhen2	probably damaging with a score of 0.996 / 0.985
SNAP	non-neutral, RI = 1
MutationTaster	disease causing
⇒ prediction: non-neutral

Thr-266-Ala

<figure id="T266A">

Mutation of threonine to alanine at position 266.

</figure>

Properties	threonine is small, neutral, polar and hydrophobic
	alanine is small, non-polar, neutral and hydrophobic
Substitution Matrices	middle ranged value &rarr neutral substitution
Structure	HELIX
PSSM	Threonine seems to be conserved with a value of 43. Alanine has a value of 29.
SIFT	AFFECT PROTEIN FUNCTION with a score of 0.00.
PolyPhen2	probably damaging with a score of 1.000
SNAP	neutral, RI = 2
MutationTaster	disease causing
⇒ prediction: non-neutral

Prediction

SNP-Prediction
SNP	Prediction	Validation
Ala259Val	neutral/non-neutral???		HGMD
Arg123Ile	non-neutral	?	dbSNP
Gln20Leu	neutral	wrong	HGMD
Gln172His	neutral	?	dbSNP
Gly103Ser	neutral	wrong	HGMD
Ile421Thr	non-neutral	?	dbSNP
Lys341Thr	non-neutral	correct	HGMD
Phe392Ser	non-neutral	?	dnSNP
Pro416Gln	non-neutral	correct	HGMD
Thr266Ala	non-neutral	correct	dbSNP

References

<references/>