UniProtKB/SwissProt variant VAR

Variant information

Variant position:

125

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 Glycine (G) to Arginine (R) at position 125 (G125R, p.Gly125Arg).

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 glycine (G) to large size and basic (R)

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.

Any additional useful information about the variant.

Sequence information

Variant position:

125

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:

GGSCKDDINSYECWCPFGFE G KNCELDVTCNIKNGRCEQFC

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                         GGSCKDDINSYECWCPFGFEGKNCELDVTCNIKNGRCEQFC

                              DGVCKDDINSYECWCRAGFEGKNCELDVTCNIKNGRCKQFC

Chimpanzee                    GGSCKDDINSYECWCPFGFEGKNCELDVTCNIKNGRCEQFC

Mouse                         GGICKDDISSYECWCQVGFEGRNCELDATCNIKNGRCKQFC

Rat                           GGICKDDINSYECWCQAGFEGRNCELDATCSIKNGRCKQFC

Bovine                        GGMCKDDINSYECWCQAGFEGTNCELDATCSIKNGRCKQFC

Cat                           GGICKDDINSYECWCQTGFEGKNCELDVTCNIKNGRCKQFC

Chicken                       GAVCKDGVSSYECMCPPGYGGRNCEIDSTCATKNGGCEHFC

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	47 – 461	Coagulation factor IX
Chain	47 – 191	Coagulation factor IXa light chain
Domain	93 – 129	EGF-like 1; calcium-binding
Metal binding	110 – 110	Calcium 7
Metal binding	111 – 111	Calcium 7; via carbonyl oxygen
Modified residue	110 – 110	(3R)-3-hydroxyaspartate
Modified residue	114 – 114	Phosphoserine
Glycosylation	107 – 107	O-linked (Fuc...) serine
Disulfide bond	119 – 128
Alternative sequence	93 – 130	Missing. In isoform 2.
Turn	125 – 128

Literature citations

Molecular analyses in hemophilia B families: identification of six new mutations in the factor IX gene.
Espinos C.; Casana P.; Haya S.; Cid A.R.; Aznar J.A.;
Haematologica 88:235-236(2003)
Cited for: VARIANTS HEMB TRP-43; ARG-84; ARG-125; VAL-125; PHE-170; ARG-302; MET-342; LEU-344; LEU-395; THR-414; TYR-435; GLU-442 AND TRP-449;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot P00740: Variant p.Gly125Arg