Difference between revisions of "Sequence-based mutation analysis (Phenylketonuria)"
From Bioinformatikpedia
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! style="background:#90EE90;" | AA - one letter |
! style="background:#90EE90;" | AA - one letter |
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! style="background:#90EE90;" | Nucleotides |
! style="background:#90EE90;" | Nucleotides |
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− | ! style="background:#90EE90;" | Properties |
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− | |Ala259Val || A259V || C776T |
+ | |Ala259Val || A259V || C776T |
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− | |Arg123Ile || R123I || G368T |
+ | |Arg123Ile || R123I || G368T |
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− | |Gln20Leu || Q20L || A59T |
+ | |Gln20Leu || Q20L || A59T |
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− | |Gly103Ser || G103S || G307A |
+ | |Gly103Ser || G103S || G307A |
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− | |His64Asn || H64N || C190A |
+ | |His64Asn || H64N || C190A |
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− | |Ile421Thr || I421T || T1262C |
+ | |Ile421Thr || I421T || T1262C |
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− | |Lys341Thr || K341T || A1022C |
+ | |Lys341Thr || K341T || A1022C |
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− | |Phe392Ser || F392S || T1175C |
+ | |Phe392Ser || F392S || T1175C |
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− | |Pro416Gln || P416Q || C1247A |
+ | |Pro416Gln || P416Q || C1247A |
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− | |Thr266Ala || T266A || A796C |
+ | |Thr266Ala || T266A || A796C |
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Revision as of 15:33, 27 June 2013
Contents
Summary
...
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: 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
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: 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
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
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
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
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: 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
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: 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
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: 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
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: 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
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: 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
SNP-Prediction | ||
---|---|---|
SNP | Prediction | Validation |
Ala259Val | ||
Arg123Ile | ||
Gln20Leu | ||
Gly103Ser | ||
His64Asn | ||
Ile421Thr | ||
Lys341Thr | ||
Phe392Ser | ||
Pro416Gln | ||
Thr266Ala |
References
<references/>