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