Biased nsSNPs in Sunyaev dataset. Original dataset downloaded from http://www.bork.embl-heidelberg.de/SNPs
Protein
ID |
Protein |
Position |
Old aa |
New aa |
Reason
for judging nsSNP as biased |
HLA |
|||||
P16188 |
HLA
class I |
176 |
W |
R |
structure
shows it is peptide-binding groove |
P10314 |
HLA
class I |
180 |
L |
Q |
structure
shows it is in peptide-binding groove |
P01892 |
HLA
class I |
121 |
R |
M |
maps to
floor of peptide-binding groove. |
P01892 |
HLA
class I |
176 |
V |
E |
maps to
peptide-binding groove |
P01892 |
HLA
class I |
33 |
F |
Y |
floor of
peptide binding groove, facing antigen |
P01892 |
HLA
class I |
180 |
L |
Q |
structure
shows it is in peptide-binding groove |
P01892 |
HLA
class I |
260 |
A |
E |
at
interface between alpha and beta chain. |
P01891 |
HLA
class I |
138 |
H |
R |
floor of
peptide-binding groove |
P16188 |
HLA
class I |
180 |
L |
W |
in
peptide-binding groove |
P01891 |
HLA
class I |
140 |
Y |
D |
floor of
peptide binnding groove |
P30512 |
HLA
class I |
126 |
H |
D |
on floor
of peptide binding groove but AWAY from groove (but not crystallized with
antigen) |
P30457 |
HLA
class I |
28 |
S |
W |
floor of
peptide binding groove but residue is facing AWAY from groove. |
P30450 |
HLA
class I |
140 |
D |
N |
amino
acid in and facing peptide groove |
P04439 |
HLA
class I |
181 |
E |
V |
amino
acid in peptide-binding cleft and facing inwards |
P01892 |
HLA
class I |
90 |
K |
N |
maps to
peptide-binding groove |
P30453 |
HLA
class I |
138 |
Q |
R |
maps to
peptide binding groove and facing in towards antigen |
P30453 |
HLA
class I |
121 |
R |
I |
maps to
peptide-binding groove and facing inwards |
P01891 |
HLA
class I |
121 |
R |
M |
maps to
peptide biinding groove and facing towards antigen |
Variant first found in disease individual |
|||||
P15154 |
rac1 |
93 |
V |
G |
Oncogene
19(26)3013-20, mutations could have come from cancer cells (and the protein
is a tumor suppressor) |
P15154 |
rac1 |
44 |
V |
A |
Oncogene
19(26)3013-20, mutations could have come from cancer cells (and the protein
is a tumor suppressor) |
P15154 |
rac1 |
59 |
A |
T |
Oncogene
19(26)3013-3020 could have come from cancer cells |
P15154 |
rac1 |
63 |
D |
G |
Oncogene;
19(26)3013-20 mutations could have come from cancer cells |
P15154 |
rac1 |
98 |
Y |
C |
Oncogene
19(26)3013-20 mutations could have come from cancer cells |
P21181 |
G25K,
a GTP-binding protein |
14 |
V |
A |
Some
kind of discrepancy here. Sunyaev has this as belonging to P21181, but
according to HGBASE, this is in rac1 from cancer cells (Oncogene 19:3013-20). |
P02042 |
hemoglobin
delta |
141 |
L |
P |
from
Greek Cypriot families suspected of having delta-thalassemia |
P02042 |
hemoglobin
delta |
24 |
G |
D |
identified
in a patient with beta-thalassemia |
P02042 |
hemoglobin
delta |
98 |
V |
M |
sequenced
a black male who had HPFH |
P02042 |
hemoglobin
delta |
116 |
R |
C |
Blood
1991 78(12):3298-305 from families suspected of having delta-thalassemia |
P02042 |
hemoglobin
delta |
99 |
D |
N |
found
in beta-thalassema patient |
P06276 |
cholinesterase |
98 |
D |
G |
PNAS
86:953-7 Pharmacogenetics:Hereditary & Response to Drugs Kalow (1966)
p.69 first identified in patients with low cholinesterase activity |
P15559 |
NADPH
dehydrogenase |
187 |
P |
S |
Associated
with lung cancer |
P11387 |
DNA
topoisomerase I |
533 |
D |
G |
NAR
19:69-75- not found in a natural population. Leukemia cell line -> CPT
resistant line (CPT-K5) , sequenced |
P05062 |
fructose-bisphosphate
aldolase b |
149 |
A |
P |
found
in individual with hereditary fructose intolerance |
O75931 |
Immune-hemochromatosis
splice variant |
180 |
C |
Y |
Nat.
Genet 13:399- positional cloning approach 85% of paitents. Associated w/
hemochromatosis |
P01011 |
alpha-1
anitichymotrypsin |
78 |
L |
P |
German
family with COPD |
In vitro mutagenesis |
|||||
P03372 |
estrogen
receptor |
447 |
C |
A |
Journal
of Biol Chem 199 June 15 266(17):10880-7 from an in vitro mutagenesis study |
P03372 |
estrogen
receptor |
400 |
G |
V |
EMBO
J Vol 8 1981-1986 -- clone artefactual point mutation |
P03372 |
estrogen
receptor |
364 |
V |
E |
V364E
Mol Endocriinology 1996 Dec 10(12):1519-26 regional chemical mutagenesis |