UniProtKB/Swiss-Prot P07225: Variant p.Thr78Met

• Variant information
• Sequence information
• Literature citations
• All

Variant information

Variant position: 78 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Type of variant: LP/P [Disclaimer: Variants classification is intended for research purposes only, not for clinical and diagnostic use. The label disease variant is assigned according to literature reports on probable disease-association that can be based on theoretical reasons. This label must not be considered as a definitive proof for the pathogenic role of a variant.] 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 Threonine (T) to Methionine (M) at position 78 (T78M, p.Thr78Met). 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 polar (T) to medium size and hydrophobic (M) 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 THPH5; reduces expression of PROS1 by 33.2% (P < 0.001) and activity by 3.6-fold; has only a modest 1.5-fold (P < 0.001) reduced affinity for phospholipid and an antibody specific for the Ca(2+)-dependent conformation of the PROS1 Gla domain. Any additional useful information about the variant.
Other resources: Links to websites of interest for the variant.

• Variant rs6122 [ dbSNP | Ensembl ]

Sequence information

Variant position: 78 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length: 676 The length of the canonical sequence.
Location on the sequence: CIEELCNKEEAREVFENDPE T DYFYPKYLVCLRSFQTGLFT 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.
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	42 – 676	Vitamin K-dependent protein S
Domain	42 – 87	Gla
Modified residue	60 – 60	4-carboxyglutamate
Modified residue	61 – 61	4-carboxyglutamate
Modified residue	66 – 66	4-carboxyglutamate
Modified residue	67 – 67	4-carboxyglutamate
Modified residue	70 – 70	4-carboxyglutamate
Modified residue	73 – 73	4-carboxyglutamate
Modified residue	77 – 77	4-carboxyglutamate

Literature citations

Identification of 15 different candidate causal point mutations and three polymorphisms in 19 patients with protein S deficiency using a scanning method for the analysis of the protein S active gene.
Gandrille S.; Borgel D.; Eschwege-Gufflet V.; Aillaud M.; Dreyfus M.; Matheron C.; Gaussem P.; Abgrall J.F.; Jude B.; Sie P.; Toulon P.; Aiach M.;
Blood 85:130-138(1995)
Cited for: VARIANTS THPH5 LEU-40; HIS-41; ALA-67; CYS-72; MET-78; HIS-90; ASN-144; GLY-245; LYS-249; TRP-265; ARG-265 AND ASN-376; VARIANTS LEU-76 AND VAL-385; Protein S Gla-domain mutations causing impaired Ca(2+)-induced phospholipid binding and severe functional protein S deficiency.
Rezende S.M.; Lane D.A.; Mille-Baker B.; Samama M.M.; Conard J.; Simmonds R.E.;
Blood 100:2812-2819(2002)
Cited for: VARIANTS THPH5 ASP-52 AND MET-78; CHARACTERIZATION OF VARIANTS THPH5 ASP-52 AND MET-78;