Difference between revisions of "Gaucher Disease: Task 08 - Sequence-based mutation analysis"

From Bioinformatikpedia
(Physicochemical properties and changes of 10 Mutations)
(Physicochemical properties and changes of 10 Mutations)
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! style="background:#efefef;" | Charge (pH)
 
! style="background:#efefef;" | Charge (pH)
 
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| [http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=371238435 rs371238435] || 465 || CCT ⇒ TCT || 14 || Pro ⇒ Ser || P14S ||||
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| [http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=371238435 rs371238435] || 465 || <span style="color:#FF0040">'''C'''</span>CT ⇒ TCT || 14 || Pro ⇒ Ser || P14S ||||
 
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| CM057078 || - ||A<span style="color:#DF013A">'''G'''</span>C ⇒ A<span style="color:#FF0040">'''T'''</span>C ||51 || Ser ⇒ Ile || S51I || polar ⇒ nonpolar || neutral ⇒ neutral
+
| CM057078 || - ||A<span style="color:#FF0040">'''G'''</span>C ⇒ A<span style="color:#FF0040">'''T'''</span>C ||51 || Ser ⇒ Ile || S51I || polar ⇒ nonpolar || neutral ⇒ neutral
 
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| [http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=368786234 rs368786234] || 656 || AGCAGA || 77 || Ser ⇒ Arg || S77R || ||
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| [http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=368786234 rs368786234] || 656 || AG<span style="color:#FF0040">'''C'''</span>AG<span style="color:#FF0040">'''A'''</span> || 77 || Ser ⇒ Arg || S77R || ||
 
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| [http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=374003673 rs374003673] || 847 || AATAGT || 141 || Asn ⇒ Ser || N141S || ||
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| [http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=374003673 rs374003673] || 847 || A<span style="color:#FF0040">'''A'''</span>TA<span style="color:#FF0040">'''G'''</span>T || 141 || Asn ⇒ Ser || N141S || ||
 
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| CM880035 ||- ||C'''G'''G ⇒ C'''A'''G || 159 || Arg ⇒ Gln || R159Q || polar ⇒ polar || positve ⇒ neutral
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| CM880035 ||- ||C<span style="color:#FF0040">'''G'''</span>G ⇒ C<span style="color:#FF0040">'''A'''</span>G || 159 || Arg ⇒ Gln || R159Q || polar ⇒ polar || positve ⇒ neutral
 
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| [http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=374591570 rs374591570] || 1062 || CTCTTC || 213 || Leu ⇒ Phe || L213F || ||
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| [http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=374591570 rs374591570] || 1062 || <span style="color:#FF0040">'''C'''</span>TC<span style="color:#FF0040">'''T'''</span>TC || 213 || Leu ⇒ Phe || L213F || ||
 
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| CM992894 ||- || G'''G'''A ⇒ GAA||241 || Gly ⇒ Glu || G241E || nonpolar ⇒ polar || neutral ⇒ negative
+
| CM992894 ||- || G<span style="color:#FF0040">'''G'''</span>A ⇒ G<span style="color:#FF0040">'''A'''</span>A||241 || Gly ⇒ Glu || G241E || nonpolar ⇒ polar || neutral ⇒ negative
 
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| [http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=371083513 rs371083513] || 1470 || GTAATA ||349 || Val ⇒ Ile || V349I || ||
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| [http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=371083513 rs371083513] || 1470 || <span style="color:#FF0040">'''G'''</span>TA<span style="color:#FF0040">'''A'''</span>TA ||349 || Val ⇒ Ile || V349I || ||
 
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| CM960697 ||- || A'''C'''G ⇒ A'''T'''G || 408|| Thr ⇒ Met || T408M || polar ⇒ nonpolar || neutral ⇒ neutral
+
| CM960697 ||- || A<span style="color:#FF0040">'''C'''</span>G ⇒ A<span style="color:#FF0040">'''T'''</span>G || 408|| Thr ⇒ Met || T408M || polar ⇒ nonpolar || neutral ⇒ neutral
 
|-
 
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| CM057072 ||- || A'''A'''C ⇒ A'''G'''C|| 501|| Asn ⇒ Ser || N501S || polar ⇒ polar || neutral ⇒ neutral
+
| CM057072 ||- || A<span style="color:#FF0040">'''A'''</span>C ⇒ A<span style="color:#FF0040">'''G'''</span>C|| 501|| Asn ⇒ Ser || N501S || polar ⇒ polar || neutral ⇒ neutral
 
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|-
 
|}
 
|}

Revision as of 14:55, 6 August 2013

LabJournal

Physicochemical properties and changes of 10 Mutations

Mutations
mRNA Protein Properties
Reference Sequence Position Codon change Codon Number Amino Acid change One letter code Polarity Charge (pH)
rs371238435 465 CCT ⇒ TCT 14 Pro ⇒ Ser P14S
CM057078 - AGC ⇒ ATC 51 Ser ⇒ Ile S51I polar ⇒ nonpolar neutral ⇒ neutral
rs368786234 656 AGC ⇒ AGA 77 Ser ⇒ Arg S77R
rs374003673 847 AAT ⇒ AGT 141 Asn ⇒ Ser N141S
CM880035 - CGG ⇒ CAG 159 Arg ⇒ Gln R159Q polar ⇒ polar positve ⇒ neutral
rs374591570 1062 CTC ⇒ TTC 213 Leu ⇒ Phe L213F
CM992894 - GGA ⇒ GAA 241 Gly ⇒ Glu G241E nonpolar ⇒ polar neutral ⇒ negative
rs371083513 1470 GTA ⇒ ATA 349 Val ⇒ Ile V349I
CM960697 - ACG ⇒ ATG 408 Thr ⇒ Met T408M polar ⇒ nonpolar neutral ⇒ neutral
CM057072 - AAC ⇒ AGC 501 Asn ⇒ Ser N501S polar ⇒ polar neutral ⇒ neutral


short summary

Mutations inside the structure

pymol-image inside/outside secondary structure

Substitution and Phenotype

blossom

PSSM

Multiple Sequence Alignment

Comparison of different approaches

SIFT, Polyphen, Mutationtaster, SNAP -> one table

References

http://en.wikipedia.org/wiki/Amino_acid

hgmd

[GENE%20AND%20%22human%22[ORGN]%20AND%20%22snp%22[SNP_CLASS]%20&cmd=DetailsSearch dbSNP]