UniProtKB/SwissProt variant VAR

Variant information

Variant position:

1062

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 Alanine (A) to Threonine (T) at position 1062 (A1062T, p.Ala1062Thr).

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 small size and hydrophobic (A) to medium size and polar (T)

The physico-chemical property of the reference and variant residues and the change implicated.

BLOSUM score:

0

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:

Increased incidence in sporadic acute myeloid leukemia.

Any additional useful information about the variant.

Other resources:

Links to websites of interest for the variant.

Variant rs35719940 [ dbSNP | Ensembl ]

Sequence information

Variant position:

1062

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

Protein sequence length:

1132

The length of the canonical sequence.

Location on the sequence:

LCYSILKAKNAGMSLGAKGA A GPLPSEAVQWLCHQAFLLKL

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                         LCYSILKAKNAGMSLGAKGAAGPLPSEAVQWL-----------------CHQAFLLKL

                              CCYSLLKARNAGLSLGAKGASGLFPSEAARWL---------

Mouse                         CCYAILKVKNPGMTLKA---SGSFPPEAAHWL---------

Rat                           CCYAILKVKNPGVSLRAKGAPGSFPPEATRWL---------

Bovine                        RGYALLKARNAGASLGARGAAGLFPSEAAQWL---------

Baker's yeast                 SGCPITK-------------CDPLIEYEVRFT---------

Fission yeast                 LGYTSRR---------------FLSSAEVKWLFCLGMRDGL

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 – 1132	Telomerase reverse transcriptase
Region	936 – 1132	CTE
Alternative sequence	808 – 1132	Missing. In isoform 2 and isoform 4.

Literature citations

Submission
NIEHS SNPs program;
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]; VARIANTS TYR-412 AND THR-1062;

Mutations in TERT, the gene for telomerase reverse transcriptase, in aplastic anemia.
Yamaguchi H.; Calado R.T.; Ly H.; Kajigaya S.; Baerlocher G.M.; Chanock S.J.; Lansdorp P.M.; Young N.S.;
N. Engl. J. Med. 352:1413-1424(2005)
Cited for: VARIANTS PFBMFT1 THR-202; TYR-412; MET-694; CYS-772 AND MET-1090; VARIANTS THR-279; GLU-441 DEL AND THR-1062;

Defining the pathogenic role of telomerase mutations in myelodysplastic syndrome and acute myeloid leukemia.
Kirwan M.; Vulliamy T.; Marrone A.; Walne A.J.; Beswick R.; Hillmen P.; Kelly R.; Stewart A.; Bowen D.; Schonland S.O.; Whittle A.M.; McVerry A.; Gilleece M.; Dokal I.;
Hum. Mutat. 30:1567-1573(2009)
Cited for: VARIANTS ALA-65; MET-299; LYS-522 AND THR-1062; VARIANTS AA THR-202; TYR-412; GLU-441 DEL; ASN-570; GLN-631; MET-694 AND LEU-785;

Constitutional hypomorphic telomerase mutations in patients with acute myeloid leukemia.
Calado R.T.; Regal J.A.; Hills M.; Yewdell W.T.; Dalmazzo L.F.; Zago M.A.; Lansdorp P.M.; Hogge D.; Chanock S.J.; Estey E.H.; Falcao R.P.; Young N.S.;
Proc. Natl. Acad. Sci. U.S.A. 106:1187-1192(2009)
Cited for: VARIANTS ALA-65; MET-299; TYR-412; GLU-441 DEL; LYS-522 AND THR-1062;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot O14746: Variant p.Ala1062Thr