UniProtKB/SwissProt variant VAR

Variant information

Variant position:

229

The position of the amino-acid change on the UniProtKB canonical protein sequence.

Type of variant:

US

The variants are classified into three categories: LP/P, LB/B and US.

LP/P: likely pathogenic or pathogenic.
LB/B: likely benign or benign.
US: uncertain significance

Residue change:

From Serine (S) to Tyrosine (Y) at position 229 (S229Y, p.Ser229Tyr).

Indicates the amino acid change of the variant. The one-letter and three-letter codes for amino acids used in UniProtKB/Swiss-Prot are those adopted by the commission on Biochemical Nomenclature of the IUPAC-IUB.

Physico-chemical properties:

Change from small size and polar (S) to large size and aromatic (Y)

The physico-chemical property of the reference and variant residues and the change implicated.

BLOSUM score:

-2

The score within a Blosum matrix for the corresponding wild-type to variant amino acid change. The log-odds score measures the logarithm for the ratio of the likelihood of two amino acids appearing by chance. The Blosum62 substitution matrix is used. This substitution matrix contains scores for all possible exchanges of one amino acid with another:

Lowest score: -4 (low probability of substitution).
Highest score: 11 (high probability of substitution).

More information can be found on the following page

Variant description:

In a lung large cell carcinoma sample; somatic mutation.

Any additional useful information about the variant.

Sequence information

Variant position:

229

The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:

983

The length of the canonical sequence.

Location on the sequence:

LAMFPDTVPMDSQSLVEVRG S CVNNSKEEDPPRMYCSTEGE

The residue change on the sequence. Unless the variant is located at the beginning or at the end of the protein sequence, both residues upstream (20) and downstream (20) of the variant will be shown.

Residue conservation:

The multiple alignment of the region surrounding the variant against various orthologous sequences.

Human                         LAMFPDTVPMDSQSLVEVRGSCVNNSKEEDPPRMYCSTEGE

Mouse                         LAMFPDTVPMDSQSLVEVRGSCVNNSKEEDPPRMYCSTEGE

Rat                           LAMFPDTVPMDSQSLVEVRGSCVNNSKEEDPPRMYCSTEGE

Chicken                       LAMFPDTVPMDSQSLVEVRGSCVNHSKEEEPPKMYCSTEGE

Zebrafish                     LARFPDTVTGGDSALVEVRGTCVEDAEELEGPRMFCSADGG

Sequence annotation in neighborhood:

The regions or sites of interest surrounding the variant. In general the features listed are posttranslational modifications, binding sites, enzyme active sites, local secondary structure or other characteristics reported in the cited references. The "Sequence annotation in neighborhood" lines have a fixed format:

Type: the type of sequence feature.
Positions: endpoints of the sequence feature.
Description: contains additional information about the feature.

Type	Positions	Description
Chain	21 – 983	Ephrin type-A receptor 3
Topological domain	21 – 541	Extracellular
Glycosylation	232 – 232	N-linked (GlcNAc...) asparagine

Literature citations

Patterns of somatic mutation in human cancer genomes.
Greenman C.; Stephens P.; Smith R.; Dalgliesh G.L.; Hunter C.; Bignell G.; Davies H.; Teague J.; Butler A.; Stevens C.; Edkins S.; O'Meara S.; Vastrik I.; Schmidt E.E.; Avis T.; Barthorpe S.; Bhamra G.; Buck G.; Choudhury B.; Clements J.; Cole J.; Dicks E.; Forbes S.; Gray K.; Halliday K.; Harrison R.; Hills K.; Hinton J.; Jenkinson A.; Jones D.; Menzies A.; Mironenko T.; Perry J.; Raine K.; Richardson D.; Shepherd R.; Small A.; Tofts C.; Varian J.; Webb T.; West S.; Widaa S.; Yates A.; Cahill D.P.; Louis D.N.; Goldstraw P.; Nicholson A.G.; Brasseur F.; Looijenga L.; Weber B.L.; Chiew Y.-E.; DeFazio A.; Greaves M.F.; Green A.R.; Campbell P.; Birney E.; Easton D.F.; Chenevix-Trench G.; Tan M.-H.; Khoo S.K.; Teh B.T.; Yuen S.T.; Leung S.Y.; Wooster R.; Futreal P.A.; Stratton M.R.;
Nature 446:153-158(2007)
Cited for: VARIANTS [LARGE SCALE ANALYSIS] TYR-229; PHE-449; LEU-518; VAL-564; SER-568; PRO-590; GLU-766; GLY-777; HIS-914 AND ARG-924;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot P29320: Variant p.Ser229Tyr