UniProtKB/SwissProt variant VAR

Variant information

Variant position:

52

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 Glycine (G) to Glutamate (E) at position 52 (G52E, p.Gly52Glu).

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 glycine (G) to medium size and acidic (E)

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

Involvement in disease:

Treacher Collins syndrome 2 (TCS2) [MIM:613717]: A form of Treacher Collins syndrome, a disorder of craniofacial development. Treacher Collins syndrome is characterized by a combination of bilateral downward slanting of the palpebral fissures, colobomas of the lower eyelids with a paucity of eyelashes medial to the defect, hypoplasia of the facial bones, cleft palate, malformation of the external ears, atresia of the external auditory canals, and bilateral conductive hearing loss. {ECO:0000269|PubMed:21131976}. 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 TCS2.

Any additional useful information about the variant.

Sequence information

Variant position:

52

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

Protein sequence length:

133

The length of the canonical sequence.

Location on the sequence:

AAGTDRHCVTFVLHEEDHTL G NSLRYMIMKNPEVEFCGYTT

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                         AAGT---------------------DRHCVTFVLHEEDHTLGNSLRYMIMKNPEVEFCGYTT

Mouse                         AAGT---------------------DRQCVTFVLHEEDHTL

Bovine                        AAGT---------------------DRHCVTFVLHEEDHTL

Xenopus laevis                AQGN---------------------EESCVTFVLHEEDHTL

Zebrafish                     TDGA---------------------DEGCVTFVLNEEDHTL

Caenorhabditis elegans        VDDEEDLNVPSKKKMEILDPKSFEQDPSNLTLIMYEEDHTI

Drosophila                    LAGDE------------------KNGEGSRTFVFTNEGHTL

Baker's yeast                 MTGDEEQEEEPDREKIKLLTQATSEDGTSASFQIVEEDHTL

Fission yeast                 LPGH-------------------SADLTSVTFQIQKEDHTL

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 – 133	DNA-directed RNA polymerases I and III subunit RPAC2

Literature citations

Mutations in genes encoding subunits of RNA polymerases I and III cause Treacher Collins syndrome.
Dauwerse J.G.; Dixon J.; Seland S.; Ruivenkamp C.A.; van Haeringen A.; Hoefsloot L.H.; Peters D.J.; Boers A.C.; Daumer-Haas C.; Maiwald R.; Zweier C.; Kerr B.; Cobo A.M.; Toral J.F.; Hoogeboom A.J.; Lohmann D.R.; Hehr U.; Dixon M.J.; Breuning M.H.; Wieczorek D.;
Nat. Genet. 43:20-22(2011)
Cited for: VARIANTS TCS2 LYS-47; ILE-50; ARG-51; GLU-52; CYS-56; SER-82 AND SER-99;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot P0DPB6: Variant p.Gly52Glu