UniProtKB/SwissProt variant VAR

Variant information

Variant position:

1082

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

Type of variant:

US

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 Histidine (H) to Leucine (L) at position 1082 (H1082L, p.His1082Leu).

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 (H) to medium size and hydrophobic (L)

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

Variant description:

In AT; unknown pathological significance.

Any additional useful information about the variant.

Sequence information

Variant position:

1082

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

Protein sequence length:

3056

The length of the canonical sequence.

Location on the sequence:

NVMGKDFPVNEVFTQFLADN H HQVRMLAAESINRLFQDTKG

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                         NVMGKDFPVNEVFTQFLADNHHQVRMLAAESINRLFQDTK-G

Mouse                         NVKGQDFPVNEAFSQFLADDHHQVRMLAAGSVNRLFQDMRQ

Pig                           NVMEKDFPVNEVFPQFLADNHHQVCMLAAGLINRLFQHMKQ

Caenorhabditis elegans        ---------GKELSGYTLDPY----TVAANVHNVHFDHINV

Drosophila                    YLLENFAVICKSTAKFITMPTLEVRFATLFTFTILLESNCV

Baker's yeast                 SMLLLSLLQNHDLSHGSIRGGKQRVFAT---FIKCLQKLDS

Fission yeast                 KFIFQLSPTSHVYSKF---DYQKLISLTLKDSDVCVIYNFV

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	2 – 3056	Serine-protein kinase ATM

Literature citations

Ataxia-telangiectasia: phenotype/genotype studies of ATM protein expression, mutations, and radiosensitivity.
Becker-Catania S.G.; Chen G.; Hwang M.J.; Wang Z.; Sun X.; Sanal O.; Bernatowska-Matuszkiewicz E.; Chessa L.; Lee E.Y.-H.P.; Gatti R.A.;
Mol. Genet. Metab. 70:122-133(2000)
Cited for: VARIANTS AT 35-ARG--VAL-3056 DEL; CYS-49; 292-LEU; 393-TRP--VAL-3056 DEL; LEU-1082; 1171-GLN--VAL-3056 DEL; 1839-GLN--VAL-3056 DEL; GLU-2063; CYS-2227; 2246-CYS--THR-2252 DELINS HIS; 2547-AER--SER-2549 DEL; GLU-2625 AND PRO-2626;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q13315: Variant p.His1082Leu