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UniProtKB/Swiss-Prot P16109: Variant p.Leu640Val

P-selectin
Gene: SELP
Variant information

Variant position:  640
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 Valine (V) at position 640 (L640V, p.Leu640Val).
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:  1
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:  Associated with susceptibility to ischemic stroke.
Any additional useful information about the variant.

Other resources:  
Links to websites of interest for the variant.



Sequence information

Variant position:  640
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:  830
The length of the canonical sequence.

Location on the sequence:   GRWSATPPTCKGIASLPTPG  L QCPALTTPGQGTMYCRHHPG
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                         GRWSATPPTCK-GIASLPTPGLQCPALTTPGQGTMYCRHHPG

Mouse                         GRWSAPPPTCK-GITSLPAPAVRCPALTTPGQGTMSCQHHL

Rat                           GRWSAPPPTCK-GVTSLPVPSVRCPALTTPGQGTMSCRHHL

Bovine                        ------------DTVSAPAPGVQCPTLIAPKQGTMSCQHHV

Sheep                         GRWTAPPPSCKVDTVSAPAPGLRCPSLIAPNQGTMSCQHHL

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.

TypePositionsDescription
Chain 42 – 830 P-selectin
Topological domain 42 – 771 Extracellular
Domain 640 – 701 Sushi 8


Literature citations

Submission
SeattleSNPs variation discovery resource;
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]; VARIANTS ARG-179; MET-209; PHE-230; ILE-274; ASN-331; LEU-385; LYS-542; ASN-603; ALA-619; VAL-631; VAL-640; ASN-661; SER-673 AND PRO-756;

The DNA sequence and biological annotation of human chromosome 1.
Gregory S.G.; Barlow K.F.; McLay K.E.; Kaul R.; Swarbreck D.; Dunham A.; Scott C.E.; Howe K.L.; Woodfine K.; Spencer C.C.A.; Jones M.C.; Gillson C.; Searle S.; Zhou Y.; Kokocinski F.; McDonald L.; Evans R.; Phillips K.; Atkinson A.; Cooper R.; Jones C.; Hall R.E.; Andrews T.D.; Lloyd C.; Ainscough R.; Almeida J.P.; Ambrose K.D.; Anderson F.; Andrew R.W.; Ashwell R.I.S.; Aubin K.; Babbage A.K.; Bagguley C.L.; Bailey J.; Beasley H.; Bethel G.; Bird C.P.; Bray-Allen S.; Brown J.Y.; Brown A.J.; Buckley D.; Burton J.; Bye J.; Carder C.; Chapman J.C.; Clark S.Y.; Clarke G.; Clee C.; Cobley V.; Collier R.E.; Corby N.; Coville G.J.; Davies J.; Deadman R.; Dunn M.; Earthrowl M.; Ellington A.G.; Errington H.; Frankish A.; Frankland J.; French L.; Garner P.; Garnett J.; Gay L.; Ghori M.R.J.; Gibson R.; Gilby L.M.; Gillett W.; Glithero R.J.; Grafham D.V.; Griffiths C.; Griffiths-Jones S.; Grocock R.; Hammond S.; Harrison E.S.I.; Hart E.; Haugen E.; Heath P.D.; Holmes S.; Holt K.; Howden P.J.; Hunt A.R.; Hunt S.E.; Hunter G.; Isherwood J.; James R.; Johnson C.; Johnson D.; Joy A.; Kay M.; Kershaw J.K.; Kibukawa M.; Kimberley A.M.; King A.; Knights A.J.; Lad H.; Laird G.; Lawlor S.; Leongamornlert D.A.; Lloyd D.M.; Loveland J.; Lovell J.; Lush M.J.; Lyne R.; Martin S.; Mashreghi-Mohammadi M.; Matthews L.; Matthews N.S.W.; McLaren S.; Milne S.; Mistry S.; Moore M.J.F.; Nickerson T.; O'Dell C.N.; Oliver K.; Palmeiri A.; Palmer S.A.; Parker A.; Patel D.; Pearce A.V.; Peck A.I.; Pelan S.; Phelps K.; Phillimore B.J.; Plumb R.; Rajan J.; Raymond C.; Rouse G.; Saenphimmachak C.; Sehra H.K.; Sheridan E.; Shownkeen R.; Sims S.; Skuce C.D.; Smith M.; Steward C.; Subramanian S.; Sycamore N.; Tracey A.; Tromans A.; Van Helmond Z.; Wall M.; Wallis J.M.; White S.; Whitehead S.L.; Wilkinson J.E.; Willey D.L.; Williams H.; Wilming L.; Wray P.W.; Wu Z.; Coulson A.; Vaudin M.; Sulston J.E.; Durbin R.M.; Hubbard T.; Wooster R.; Dunham I.; Carter N.P.; McVean G.; Ross M.T.; Harrow J.; Olson M.V.; Beck S.; Rogers J.; Bentley D.R.;
Nature 441:315-321(2006)
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]; VARIANT VAL-640;

Submission
Mural R.J.; Istrail S.; Sutton G.G.; Florea L.; Halpern A.L.; Mobarry C.M.; Lippert R.; Walenz B.; Shatkay H.; Dew I.; Miller J.R.; Flanigan M.J.; Edwards N.J.; Bolanos R.; Fasulo D.; Halldorsson B.V.; Hannenhalli S.; Turner R.; Yooseph S.; Lu F.; Nusskern D.R.; Shue B.C.; Zheng X.H.; Zhong F.; Delcher A.L.; Huson D.H.; Kravitz S.A.; Mouchard L.; Reinert K.; Remington K.A.; Clark A.G.; Waterman M.S.; Eichler E.E.; Adams M.D.; Hunkapiller M.W.; Myers E.W.; Venter J.C.;
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]; VARIANT VAL-640;

The P-selectin gene is highly polymorphic: reduced frequency of the Pro715 allele carriers in patients with myocardial infarction.
Herrmann S.M.; Ricard S.; Nicaud V.; Mallet C.; Evans A.; Ruidavets J.B.; Arveiler D.; Luc G.; Cambien F.;
Hum. Mol. Genet. 7:1277-1284(1998)
Cited for: VARIANTS ASN-331; ASN-603; VAL-640 AND PRO-756;

Characterization of single-nucleotide polymorphisms in coding regions of human genes.
Cargill M.; Altshuler D.; Ireland J.; Sklar P.; Ardlie K.; Patil N.; Shaw N.; Lane C.R.; Lim E.P.; Kalyanaraman N.; Nemesh J.; Ziaugra L.; Friedland L.; Rolfe A.; Warrington J.; Lipshutz R.; Daley G.Q.; Lander E.S.;
Nat. Genet. 22:231-238(1999)
Cited for: VARIANTS MET-209; LEU-301; ASN-331; VAL-365; PHE-500; ASN-603; VAL-640 AND PRO-756;

Polymorphism in the P-selectin and interleukin-4 genes as determinants of stroke: a population-based, prospective genetic analysis.
Zee R.Y.L.; Cook N.R.; Cheng S.; Reynolds R.; Erlich H.A.; Lindpaintner K.; Ridker P.M.;
Hum. Mol. Genet. 13:389-396(2004)
Cited for: ASSOCIATION OF VARIANT VAL-640 WITH SUSCEPTIBILITY TO ISCHSTR;

Disclaimer: Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. They are not in any way intended to be used as a substitute for professional medical advice, diagnostic, treatment or care.