UniProtKB/SwissProt variant VAR

Variant information

Variant position:

200

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 Proline (P) to Leucine (L) at position 200 (P200L, p.Pro200Leu).

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:

-3

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

Other resources:

Links to websites of interest for the variant.

Variant rs1050450 [ dbSNP | Ensembl ]

Sequence information

Variant position:

200

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

Protein sequence length:

203

The length of the canonical sequence.

Location on the sequence:

SRRFQTIDIEPDIEALLSQG P SCA

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                         SRRFQTIDIEPDIEALLSQGPSCA-

Chimpanzee                    SRRFQTIDIEPDIEALLSQGPSCA

Mouse                         SRRFRTIDIEPDIETLLSQQSGNS

Rat                           SRRFRTIDIEPDIEALLSKQPSNP

Pig                           SRRFLTIDIEPDIEALLSQEPSSA

Bovine                        SRRFLTIDIEPDIETLLSQGASA-

Rabbit                        SRRFPTIDIEPDIQALLSKGSGGA

Caenorhabditis elegans        GPTTDPKDMEKDIKEALGEKL---

Baker's yeast                 SCMTRPLELCPIIEELLNQPPEEQ

Fission yeast                 SSISKPEHLENDIESVL-------

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	1 – 203	Glutathione peroxidase 1
Modified residue	197 – 197	Phosphoserine
Modified residue	201 – 201	Phosphoserine
Alternative sequence	99 – 203	Missing. In isoform 2.

Literature citations

Submission
NIEHS SNPs program;
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (ISOFORM 1); VARIANTS PRO-5; THR-194 AND LEU-200;

Low yield of polymorphisms from EST blast searching: analysis of genes related to oxidative stress and verification of the P197L polymorphism in GPX1.
Forsberg L.; de Faire U.; Morgenstern R.;
Hum. Mutat. 13:294-300(1999)
Cited for: VARIANT LEU-200;

Functional variants in the glutathione peroxidase-1 (GPx-1) gene are associated with increased intima-media thickness of carotid arteries and risk of macrovascular diseases in Japanese type 2 diabetic patients.
Hamanishi T.; Furuta H.; Kato H.; Doi A.; Tamai M.; Shimomura H.; Sakagashira S.; Nishi M.; Sasaki H.; Sanke T.; Nanjo K.;
Diabetes 53:2455-2460(2004)
Cited for: VARIANTS ALA-8 DEL AND LEU-200;

Increased risk of bladder cancer associated with a glutathione peroxidase 1 codon 198 variant.
Ichimura Y.; Habuchi T.; Tsuchiya N.; Wang L.; Oyama C.; Sato K.; Nishiyama H.; Ogawa O.; Kato T.;
J. Urol. 172:728-732(2004)
Cited for: VARIANT LEU-200;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot P07203: Variant p.Pro200Leu