UniProtKB/SwissProt variant VAR

Variant information

Variant position:

590

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

Type of variant:

LB/B

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 Leucine (L) to Proline (P) at position 590 (L590P, p.Leu590Pro).

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:

Similar physico-chemical property. Both residues are medium size and hydrophobic.

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

BLOSUM score:

-3

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

Other resources:

Links to websites of interest for the variant.

Variant rs56081642 [ dbSNP | Ensembl ]

Sequence information

Variant position:

590

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:

YKSKHGADEKRLHFGNGHLK L PGLRTYVDPHTYEDPTQAVH

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                         Y-KSKHGADEKRLHFGNGHLKLPGLRTYVDPHTYEDPTQAVH

Mouse                         YHKSKHSAEEKRLHFGNGHLKLPGLRTYVDPHTYEDPTQAV

Rat                           YHKSKHSSDEKRLHFGNGHLRLPGLRTYVDPHTYEDPTQAV

Chicken                       YKKSKHGTDEKRLHFGNGHLKLPGLRTYVDPHTYEDPNQAV

Zebrafish                     YIKAKQDPEEEKMQFQHGRVKLPETRTYIHPHTYEDPNQAV

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	566 – 983	Cytoplasmic
Modified residue	596 – 596	Phosphotyrosine; by autocatalysis
Modified residue	602 – 602	Phosphotyrosine; by autocatalysis
Alternative sequence	540 – 983	Missing. In isoform 2.
Mutagenesis	596 – 596	Y -> F. 10-fold suppression of kinase activity; when associated with F-602. Full kinase activity; when associated with F-602 and F-742. Full kinase activity; when associated with F-602 and A-768.
Mutagenesis	602 – 602	Y -> F. 10-fold suppression of kinase activity; when associated with F-596. Full kinase activity; when associated with F-596 and F-742. Full kinase activity; when associated with F-596 and A-768.

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.Leu590Pro