UniProtKB/SwissProt variant VAR

Variant information

Variant position:

979

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

Type of variant:

Disease [Disclaimer]

The variants are classified into three categories: Disease, Polymorphism and Unclassified.

Disease: Variants implicated in disease according to literature reports.
Polymorphism: Variants not reported to be implicated in disease.
Unclassified: Variants with uncertain implication in disease according to literature reports. Evidence against or in favor of a pathogenic role is limited and/or conflicting.

Residue change:

From Arginine (R) to Tryptophan (W) at position 979 (R979W, p.Arg979Trp).

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 large size and basic (R) to large size and aromatic (W)

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

Involvement in disease:

Dyskeratosis congenita, autosomal dominant, 2 (DKCA2) [MIM:613989]: A rare multisystem disorder caused by defective telomere maintenance. It is characterized by progressive bone marrow failure, and the clinical triad of reticulated skin hyperpigmentation, nail dystrophy, and mucosal leukoplakia. Common but variable features include premature graying, aplastic anemia, low platelets, osteoporosis, pulmonary fibrosis, and liver fibrosis among others. Early mortality is often associated with bone marrow failure, infections, fatal pulmonary complications, or malignancy. {ECO:0000269|PubMed:15885610, ECO:0000269|PubMed:16247010, ECO:0000269|PubMed:21602826}. Note=The disease is caused by mutations affecting the gene represented in this entry.

The name and a short description of the disease associated with the variant. For more information about the disease, the user can refer to OMIM, following the link provided after the disease acronym.

Variant description:

In DKCA2; shortened telomeres but no effect on telomerase catalytic activity nor on binding to TERC.

Any additional useful information about the variant.

Other resources:

Links to websites of interest for the variant.

Variant rs199422305 [ dbSNP | Ensembl ]

Sequence information

Variant position:

979

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:

TFNRGFKAGRNMRRKLFGVL R LKCHSLFLDLQVNSLQTVCT

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                         TFNRGFKAGRNMRRKLFGVLRLKCHSLFLDLQVNSLQTVCT

                              TFSQGAKPGRNMRRKLLAVLRLKCCALFLDLQVNGIHTVYM

Mouse                         TFQSVFKAGKTMRNKLLSVLRLKCHGLFLDLQVNSLQTVCI

Rat                           TFQGVSRAGKTMRYKLLSVLRLKCHGLFLDLQVNSLQTVCI

Bovine                        TFTQGFKPGRNMRRKLLAVLQLKCHGLFLDLQVNSLQTVFT

Baker's yeast                 ------KSSKGIFRSLIALFNTRISYKTIDTNLNSTNTVLM

Fission yeast                 SVELTKHMGKSFFYKILRSSLASFAQVFIDITHNSKFNSCC

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.
Helix	966 – 983

Literature citations

Mutations in the reverse transcriptase component of telomerase (TERT) in patients with bone marrow failure.
Vulliamy T.J.; Walne A.; Baskaradas A.; Mason P.J.; Marrone A.; Dokal I.;
Blood Cells Mol. Dis. 34:257-263(2005)
Cited for: VARIANT AA THR-202; VARIANTS DKCA2 TRP-979 AND LEU-1127; CHARACTERIZATION OF VARIANT AA THR-202; CHARACTERIZATION OF VARIANTS DKCA2 TRP-979 AND LEU-1127;

Functional characterization of natural telomerase mutations found in patients with hematologic disorders.
Xin Z.T.; Beauchamp A.D.; Calado R.T.; Bradford J.W.; Regal J.A.; Shenoy A.; Liang Y.; Lansdorp P.M.; Young N.S.; Ly H.;
Blood 109:524-532(2007)
Cited for: VARIANT AA ASN-570; CHARACTERIZATION OF VARIANTS ASN-570; ASP-682; ARG-721; MET-726; ASN-902; TRP-979 AND LEU-1127;

Telomere shortening and loss of self-renewal in dyskeratosis congenita induced pluripotent stem cells.
Batista L.F.; Pech M.F.; Zhong F.L.; Nguyen H.N.; Xie K.T.; Zaug A.J.; Crary S.M.; Choi J.; Sebastiano V.; Cherry A.; Giri N.; Wernig M.; Alter B.P.; Cech T.R.; Savage S.A.; Reijo Pera R.A.; Artandi S.E.;
Nature 474:399-402(2011)
Cited for: VARIANT DKCB4 SER-704; VARIANT DKCA2 TRP-979; CHARACTERIZATION OF VARIANT DKCB4 SER-704; CHARACTERIZATION OF VARIANT DKCA2 TRP-979; CATALYTIC ACTIVITY;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot O14746: Variant p.Arg979Trp