UniProtKB/SwissProt variant VAR

Variant information

Variant position:

1001

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 Leucine (L) to Glutamine (Q) at position 1001 (L1001Q, p.Leu1001Gln).

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 hydrophobic (L) to medium size and polar (Q)

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 AT; associated with T-cell acute lymphoblastic leukemia.

Any additional useful information about the variant.

Sequence information

Variant position:

1001

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:

RRDQDVCKTILNHVLHVVKN L GQSNMDSENTRDAQGQFLTV

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                         RRDQDVCKTILNHVLHVVKNLGQSNMDSENTRDAQGQFLTV

Mouse                         RRDQDVCKTILSNVLHIVTNLGQGSVDMESTRIAQGHFLTV

Pig                           RRDQDVCKTILNHVLHIVPNLCRENVDAESTRDAQGQFLTV

Caenorhabditis elegans        KRFEKYSFLLS------IRNLIVTRMIITN---------EA

Drosophila                    HQDAELMDKVVQHMPTIFYFVRHKENHLDD-------MLMA

Baker's yeast                 SSSNQAMLLLTSYIEAIRPQWLSYPEQPLN---------SD

Fission yeast                 ERDEVYLMIFI----KIFQKCVHSKLQFTD---------AT

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
Beta strand	1001 – 1003

Literature citations

ATM mutations and phenotypes in ataxia-telangiectasia families in the British Isles: expression of mutant ATM and the risk of leukemia, lymphoma, and breast cancer.
Stankovic T.; Kidd A.M.J.; Sutcliffe A.; McGuire G.M.; Robinson P.; Weber P.; Bedenham T.; Bradwell A.R.; Easton D.F.; Lennox G.G.; Haites N.; Byrd P.J.; Taylor A.M.R.;
Am. J. Hum. Genet. 62:334-345(1998)
Cited for: POSSIBLE INVOLVEMENT IN TALL; VARIANTS AT LEU-292; ASP-768; GLN-1001; ARG-1691; ILE-1743; GLY-2424; 2427-LEU-ARG-2428 DEL; 2546-SER--ILE-2548 DEL; ASP-2554; GLY-2668 AND CYS-2827;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q13315: Variant p.Leu1001Gln