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

From Bioinformatikpedia
(→‎Gln-172-His)
(→‎Analyze SNPs)
Line 66: Line 66:
 
|Structure || HELIX
 
|Structure || HELIX
 
|-
  
|-
−
|Substitution Matrices || middle ranged value -> neutral substitution
+
|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.
  
|PSSM || Alanine seems to be highly conserved with a value of 70. Valine has a value of 1.
Line 78: Line 78:
 
|MutationTaster || disease causing
  
|MutationTaster || disease causing
 
|-
  
|-
−
| colspan="2" |→ prediction = '''...'''
 +
| colspan="2" |'''⇒''' prediction: '''...'''
 
|}
  
|}
   
Line 93: Line 93:
 
|isoleucine is aliphatic, neutral, non-polar and hydrophobic
  
|isoleucine is aliphatic, neutral, non-polar and hydrophobic
 
|-
  
|-
−
|Substitution Matrices || low value -> bad substitution
 +
|Substitution Matrices || low value → bad substitution
 
|-
  
|-
 
|Structure ||LOOP
  
|Structure ||LOOP
Line 107: Line 107:
 
|MutationTaster || disease causing
  
|MutationTaster || disease causing
 
|-
  
|-
−
| colspan="2" | → prediction = '''non-neutral'''
 +
| colspan="2" | '''⇒''' prediction: '''non-neutral'''
 
|}
  
|}
   
Line 117: Line 117:
 
|leucine is aliphatic, neutral, non-polar and hydrophilic
 
|leucine is aliphatic, neutral, non-polar and hydrophilic
 
|-
  
|-
−
|Substitution Matrices || low value -> bad substitution
 +
|Substitution Matrices || low value → bad substitution
 
|-
  
|-
 
|Structure || LOOP
  
|Structure || LOOP
Line 131: Line 131:
 
|MutationTaster || disease causing
  
|MutationTaster || disease causing
 
|-
  
|-
−
|colspan="2" | → prediction = '''...'''
 +
|colspan="2" | '''⇒''' prediction: '''...'''
 
|}
  
|}
   
Line 168: Line 168:
 
| serine is small, neutral, polar and hydrophilic
  
| serine is small, neutral, polar and hydrophilic
 
|-
  
|-
−
|Substitution Matrices || middle ranged value -> neutral substitution
 +
|Substitution Matrices || middle ranged value → neutral substitution
 
|-
  
|-
 
|Structure || HELIX
  
|Structure || HELIX
Line 182: Line 182:
 
|MutationTaster || disease causing
  
|MutationTaster || disease causing
 
|-
  
|-
−
|colspan="2"|→ prediction = '''...'''
 +
|colspan="2"|'''⇒''' prediction: '''...'''
 
|}
  
|}
   
Line 193: Line 193:
 
|Properties || isoleucine is aliphatic, neutral, non-polar and hydrophobic - threonine is small, neutral, polar and hydrophobic
  
|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
+
|Substitution Matrices || low value for Blosum62, middle ranged value for PAM1/250 → bad or neutral substitution
 
|-
  
|-
 
|Structure || STRAND
  
|Structure || STRAND
Line 207: Line 207:
 
|MutationTaster || disease causing
  
|MutationTaster || disease causing
 
|-
  
|-
−
| colspan="2"|→ prediction = '''non-neutral'''
 +
| colspan="2"|'''⇒''' prediction: '''non-neutral'''
 
|}
  
|}
 
===Lys-341-Thr===
  
===Lys-341-Thr===
Line 219: Line 219:
 
| threonine is small, neutral, 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
+
|Substitution Matrices || low value for Blosum62, middle ranged value for PAM1/250 → bad or neutral substitution
 
|-
  
|-
 
|Structure || STRAND
  
|Structure || STRAND
Line 233: Line 233:
 
|MutationTaster || disease causing
  
|MutationTaster || disease causing
 
|-
  
|-
−
|colspan="2" |→ prediction = '''non-neutral'''
 +
|colspan="2" |'''⇒''' prediction: '''non-neutral'''
 
|}
  
|}
   
Line 246: Line 246:
 
| serine is small, neutral, polar and hydrophilic
  
| serine is small, neutral, polar and hydrophilic
 
|-
  
|-
−
|Substitution Matrices || low value -> bad substitution
 +
|Substitution Matrices || low value → bad substitution
 
|-
  
|-
 
|Structure || HELIX
  
|Structure || HELIX
Line 260: Line 260:
 
|MutationTaster || disease causing
  
|MutationTaster || disease causing
 
|-
  
|-
−
|colspan="2"|→ prediction = '''non-neutral'''
 +
|colspan="2"|'''⇒''' prediction: '''non-neutral'''
 
|}
  
|}
   
Line 273: Line 273:
 
|glutamine is neutral, polar and hydrophilic
  
|glutamine is neutral, polar and hydrophilic
 
|-
  
|-
−
|Substitution Matrices || low value -> bad substitution
 +
|Substitution Matrices || low value → bad substitution
 
|-
  
|-
 
|Structure || LOOP
  
|Structure || LOOP
Line 287: Line 287:
 
|MutationTaster || disease causing
  
|MutationTaster || disease causing
 
|-
  
|-
−
|colspan="2"|→ prediction = '''non-neutral'''
 +
|colspan="2"|'''⇒''' prediction: '''non-neutral'''
 
|}
  
|}
   
Line 300: Line 300:
 
|alanine is small, non-polar, neutral and hydrophobic
  
|alanine is small, non-polar, neutral and hydrophobic
 
|-
  
|-
−
|Substitution Matrices || middle ranged value for Blosum62 and high value for PAM1('''TODO'''PAM250: 11 neutral/high?) -> neutral or good substituion
 +
|Substitution Matrices || middle ranged value &rarr neutral substitution
 
|-
  
|-
 
|Structure || HELIX(ReProf)/LOOP(PsiPred)
  
|Structure || HELIX(ReProf)/LOOP(PsiPred)
Line 314: Line 314:
 
|MutationTaster || disease causing
  
|MutationTaster || disease causing
 
|-
  
|-
−
|colspan="2"|→ prediction = '''non-neutral'''
 +
|colspan="2"|'''⇒''' prediction: '''non-neutral'''
 
|}
  
|}
   

Revision as of 16:56, 2 July 2013

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
MutationTaster disease causing
⇒ prediction: ...


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
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: ...

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
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
MutationTaster disease causing
⇒ prediction: ...

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
MutationTaster disease causing
⇒ prediction: ...

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
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
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
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
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(ReProf)/LOOP(PsiPred)
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
MutationTaster disease causing
⇒ prediction: non-neutral

Prediction

SNP-Prediction
SNP Prediction Validation
Ala259Val
Arg123Ile non-neutral ?
Gln20Leu
Gln172His ?
Gly103Ser
Ile421Thr non-neutral ?
Lys341Thr non-neutral correct
Phe392Ser non-neutral ?
Pro416Gln non-neutral correct
Thr266Ala non-neutral correct

References

<references/>

Retrieved from "https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Sequence-based_mutation_analysis_(Phenylketonuria)&oldid=33273"