UniProtKB/SwissProt variant VAR

Variant information

Variant position:

340

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 Isoleucine (I) to Methionine (M) at position 340 (I340M, p.Ile340Met).

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:

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

Polymorphism:

Polymorphism at position 11 acts synergistically with different mutations in AGXT producing specific enzymatic phenotypes in HP1 patients. The combined presence of Leu-11 and Met-340 polymorphisms defines the minor AGXT allele, whereas their absence defines the major allele. The minor allele has frequencies of 20% in normal European and North American populations, and 50% in HP1 patients.

Additional information on the polymorphism described.

Variant description:

Associated with hyperoxaluria.

Any additional useful information about the variant.

Other resources:

Links to websites of interest for the variant.

Variant rs4426527 [ dbSNP | Ensembl ]

Sequence information

Variant position:

340

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

Protein sequence length:

392

The length of the canonical sequence.

Location on the sequence:

TVTTVAVPAGYDWRDIVSYV I DHFDIEIMGGLGPSTGKVLR

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                         TVTTVAVPAGYDWRDIVSYVIDHFDIEIMGGLGPSTGKVLR

Mouse                         TITTVTVPAGYNWRDIVSYVLDHFSIEISGGLGPTEERVLR

Rat                           TITTVTVPAGYNWRDIVSYVLDHFNIEISGGLGPSEDKVLR

Rabbit                        TVTTVIVPASYRWRDIVSYVMHHFGIEITGGLGPSADKVLR

Cat                           TVTTVAVPAGYDWRDIVNYVMDHFDIEITGGLGPSMGKVLR

Slime mold                    SLTTVNIPDGVDGKMVMKYLLDNFNIEIAGGIGAFAGKVWR

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 – 392	Alanine--glyoxylate aminotransferase
Binding site	360 – 360	Substrate
Helix	332 – 343

Literature citations

Identification of mutations associated with peroxisome-to-mitochondrion mistargeting of alanine/glyoxylate aminotransferase in primary hyperoxaluria type 1.
Purdue P.E.; Takada Y.; Danpure C.J.;
J. Cell Biol. 111:2341-2351(1990)
Cited for: NUCLEOTIDE SEQUENCE [MRNA]; VARIANTS LEU-11 AND MET-340; VARIANT HP1 ARG-170; SUBCELLULAR LOCATION;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot P21549: Variant p.Ile340Met