UniProtKB/Swiss-Prot P12259: Variant p.Arg534Gln

Coagulation factor V
Gene: F5
Chromosomal location: 1q23
Variant information

Variant position:  534
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Type of variant:  Polymorphism
The variants are classified into three categories: Disease, Polymorphism and Unclassified.
  • Disease: Variants have been found in patients and disease-association is reported in literature. However, this classification is not a definitive assessment of variant pathogenicity.
  • Polymorphism: No disease-association has been reported.
  • Unclassified: Variants have been found in patients but disease-association remains unclear.

Residue change:  From Arginine (R) to Glutamine (Q) at position 534 (R534Q, p.Arg534Gln).
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 large size and basic (R) to medium size and polar (Q)
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:  In Leiden; associated with thrombophilia; associated with susceptibility to Budd-Chiari syndrome; 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:  534
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:  2224
The length of the canonical sequence.

Location on the sequence:   DIASGLIGLLLICKSRSLDR  R GIQRAADIEQQAVFAVFDEN
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                         DIASGLIGLLLICKSRSLDRRGIQRAADIEQQAVFAVFDEN

Mouse                         DIASGLIGLLLICKSRSLDQRGVQRVADIEQQAVFAVFDEN

Pig                           DIASGLIGLLLICKSRSLDKRGIQRTADIEQKAVFAVFDEN

Bovine                        DLASGLIGLLLICKSRSLDRRGIQRAADIEQQAVFAVFDEN

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 29 – 2224 Coagulation factor V
Chain 29 – 737 Coagulation factor V heavy chain
Domain 348 – 684 F5/8 type A 2
Site 534 – 535 Cleavage; by activated protein C
Glycosylation 554 – 554 N-linked (GlcNAc...)


Literature citations

Submission
SeattleSNPs variation discovery resource;
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]; VARIANT LEIDEN GLN-534; VARIANTS SER-15; HIS-107; THR-413; LYS-513; SER-809; THR-817; ARG-858; ARG-865; SER-915; GLU-925; SER-969; LEU-980; GLN-1146; ILE-1285; SER-1404; ALA-1530 AND THR-2148;

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 LEIDEN GLN-534;

Mutation in blood coagulation factor V associated with resistance to activated protein C.
Bertina R.M.; Koeleman B.P.C.; Koster T.; Rosendaal F.R.; Dirven R.J.; de Ronde H.; van der Velden P.A.; Reitsma P.H.;
Nature 369:64-67(1994)
Cited for: VARIANT LEIDEN GLN-534;

Prevalence of the factor V Leiden mutation in hepatic and portal vein thrombosis.
Mahmoud A.E.A.; Elias E.; Beauchamp N.; Wilde J.T.;
Gut 40:798-800(1997)
Cited for: ASSOCIATION OF VARIANT LEIDEN GLN-534 WITH SUSCEPTIBILITY TO BUDD-CHIARI SYNDROME;

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: VARIANT LEIDEN GLN-534; VARIANTS HIS-107; THR-413; LYS-513; SER-809; THR-817; ARG-858; ARG-865; GLU-925; GLN-1146; ALA-1530; SER-1685; VAL-1749; VAL-1764; ILE-1820 AND GLY-2222;

Combinations of 4 mutations (FV R506Q, FV H1299R, FV Y1702C, PT 20210G/A) affecting the prothrombinase complex in a thrombophilic family.
Castoldi E.; Simioni P.; Kalafatis M.; Lunghi B.; Tormene D.; Girelli D.; Girolami A.; Bernardi F.;
Blood 96:1443-1448(2000)
Cited for: VARIANT FA5D CYS-1730; VARIANT LEIDEN GLN-534; VARIANT ARG-1327;

Meta-analysis of genetic studies in ischemic stroke: thirty-two genes involving approximately 18,000 cases and 58,000 controls.
Casas J.P.; Hingorani A.D.; Bautista L.E.; Sharma P.;
Arch. Neurol. 61:1652-1661(2004)
Cited for: ASSOCIATION OF VARIANT GLN-534 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.