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UniProtKB/Swiss-Prot P00740: Variant p.Leu52Ser

Coagulation factor IX
Gene: F9
Variant information

Variant position:  52
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Type of variant:  LP/P [Disclaimer]
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 Serine (S) at position 52 (L52S, p.Leu52Ser).
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 medium size and hydrophobic (L) to small size and polar (S)
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 HEMB; severe; Gla mutant.
Any additional useful information about the variant.



Sequence information

Variant position:  52
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:  461
The length of the canonical sequence.

Location on the sequence:   LDHENANKILNRPKRYNSGK  L EEFVQGNLERECMEEKCSFE
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                         LDHENANKILNRPKRYNSGKLEEFVQGNLERECMEEKCSFE

                              LDRENATKILSRPKRYNSGKLEEFVRGNLERECIEEKCSFE

Chimpanzee                    LDHENANKILNRPKRYNSGKLEEFVQGNLERECMEEKCSFE

Mouse                         LDRENATKILTRPKRYNSGKLEEFVRGNLERECIEERCSFE

Rat                           LDRENATKILTRPKRYNSGKLEEFVQGNLERECIEERCSFE

Bovine                        LDRENATKILHRPKRYNSGKLEEFVRGNLERECKEEKCSFE

Cat                           LDHEDATKVLSRPKRYNSGKLEEFVQGNLERECMEEKCSFE

Chicken                       IENKEASTVLSRTRRGNSNRLEELIPGNLERECIEEKCSFE

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 47 – 461 Coagulation factor IX
Chain 47 – 191 Coagulation factor IXa light chain
Domain 47 – 92 Gla
Metal binding 47 – 47 Calcium 1; via carbonyl oxygen
Metal binding 48 – 48 Calcium 2
Metal binding 53 – 53 Calcium 1; via 4-carboxyglutamate
Metal binding 53 – 53 Calcium 2; via 4-carboxyglutamate
Metal binding 54 – 54 Calcium 2; via 4-carboxyglutamate
Metal binding 54 – 54 Calcium 3; via 4-carboxyglutamate
Metal binding 61 – 61 Calcium 4 or magnesium 1; via 4-carboxyglutamate
Metal binding 63 – 63 Calcium 1; via 4-carboxyglutamate
Metal binding 63 – 63 Calcium 2; via 4-carboxyglutamate
Metal binding 63 – 63 Calcium 3; via 4-carboxyglutamate
Metal binding 66 – 66 Calcium 4 or magnesium 1; via 4-carboxyglutamate
Metal binding 67 – 67 Calcium 1; via 4-carboxyglutamate
Metal binding 72 – 72 Calcium 5 or magnesium 2; via 4-carboxyglutamate
Modified residue 53 – 53 4-carboxyglutamate
Modified residue 54 – 54 4-carboxyglutamate
Modified residue 61 – 61 4-carboxyglutamate
Modified residue 63 – 63 4-carboxyglutamate
Modified residue 66 – 66 4-carboxyglutamate
Modified residue 67 – 67 4-carboxyglutamate
Modified residue 72 – 72 4-carboxyglutamate
Beta strand 50 – 52


Literature citations

Molecular pathology of haemophilia B in Turkish patients: identification of a large deletion and 33 independent point mutations.
Onay U.V.; Kavakli K.; Kilinc Y.; Gurgey A.; Aktuglu G.; Kemahli S.; Ozbek U.; Caglayan S.H.;
Br. J. Haematol. 120:656-659(2003)
Cited for: VARIANTS HEMB TYR-28; LEU-43; GLN-43; SER-52; ASP-106; LYS-124; TYR-134; GLN-226; GLY-226; TRP-226; LYS-241; TYR-252; GLN-294; PHE-316; ARG-318; GLY-379; ILE-383; PHE-383; ILE-395; PHE-396; ARG-407 AND GLU-412;

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.