sunyaev

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