Assignment for the course in Biomedical informatics
1. Yes. It is pathogenic.
It's APOE.
It's not determined by a silent mutation.
Wild type: CGC (Arg) Muted: TGC (Cys)
Apolipoproteinemia E1, Familial type 3 hyperlipoproteinemia, atorvastatin response -Efficacy
2. 6
3. 10.
768
2
No
The variation of rs112034331 is deleterious. rs587778301 is tolerated.
rs112034331: NArs587778301: not provided
4. It is a silent mutation.
It is pathogenic.
It has effect on RNA splicing.
(e)
5.2
|
SNP
|
rs5743618
|
rs5743708
|
rs3775291
|
rs4986790
|
rs5743810
|
rs179008
|
rs2407992
|
rs4129009
|
|
Gene
|
TLR1
|
TLR2
|
TLR3
|
TLR4
|
TLR6
|
TLR7
|
TLR8
|
TLR10
|
|
Substitution
|
Non-synonymous
|
Non-synonymous
|
Non-synonymous
|
Non-synonymous
|
Non-synonymous
|
Non-synonymous
|
synonymous
|
Non-synonymous
|
|
Clinical significance
|
other
|
other
|
other
|
Benign
|
NA
|
NA
|
NA
|
NA
|
|
Determine amino acid subsitution
|
Ser→Lle
|
Arg→Gln
|
Leu→Phe
|
Asp→Gly
|
Ser→Pro
|
Gln→Leu
|
/
|
Lle→Val
|
|
Domain
|
LRRCT
|
TIR
|
-
|
-
|
-
|
-
|
/
|
TIR
|
|
MAF
|
0.2(C)
|
0.01(A)
|
0.23(T)
|
0.06(G)
|
0.12(A)
|
0.12(T)
|
0.28(G)
|
0.15(C)
|
|
Highest MAF
|
0.67(C)
EUR
|
0.02(A)
EUR
|
0.33(T)
EAS
|
0.13(G)
SAS
|
0.41(A)
EUR
|
0.23(T)
EUR
|
0.62(G)
EUR
|
0.27(C)
EAS
|
|
Lowest MAF
|
0.01(C)
EAS
|
0(A)
AFR/EAS/SAS
|
0.03(T)
AFR
|
0(G)
EAS
|
0(A)
EAS
|
0(T)
EAS
|
0.05(G)
AFR
|
0.01(C)
AFR
|
|
SIFT
|
1
|
0
|
0
|
0.15
|
0.56
|
0.29
|
|
0.28
|
|
Predicted effect
|
tolerated
|
deleterious
|
deleterious
|
tolerated
|
tolerated
|
tolerated
|
|
tolerated
|
rs5743317 Clinical Significance:NAMAF:0.01(G) SIFT:0.22
rs3775291 Clinical Significance: other MAF: 0.23(T) SIFT: 0
rs5743318 Clinical Significance: NA MAF:0.01(A) SIFT: 0.32
6. No. (reason)
It's in a coil region.