UniProtKB/SwissProt variant VAR

Variant information

Variant position:

880

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

Type of variant:

Unclassified

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 Alanine (A) to Threonine (T) at position 880 (A880T, p.Ala880Thr).

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:

In a pancreatic ductal adenocarcinoma sample; somatic mutation.

Any additional useful information about the variant.

Sequence information

Variant position:

880

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

Protein sequence length:

1257

The length of the canonical sequence.

Location on the sequence:

TGFANKDKQELKHAGKIATE A LENIRTIVSLTREKAFEQMY

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                         TGFANKDKQELKHAGKIATEALENIRTIVSLTREKAFEQMY

Mouse                         AGFANRDKQALKRAGKIATEAVENIRTVVSLTRERAFEQMY

Slime mold                    VKYFNNDALEVER---------------------------Y

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 – 1257	ATP-binding cassette sub-family B member 5
Domain	693 – 980	ABC transmembrane type-1 2
Alternative sequence	572 – 1257	Missing. In isoform 3.
Alternative sequence	577 – 1257	Missing. In isoform 2.

Literature citations

Core signaling pathways in human pancreatic cancers revealed by global genomic analyses.
Jones S.; Zhang X.; Parsons D.W.; Lin J.C.; Leary R.J.; Angenendt P.; Mankoo P.; Carter H.; Kamiyama H.; Jimeno A.; Hong S.M.; Fu B.; Lin M.T.; Calhoun E.S.; Kamiyama M.; Walter K.; Nikolskaya T.; Nikolsky Y.; Hartigan J.; Smith D.R.; Hidalgo M.; Leach S.D.; Klein A.P.; Jaffee E.M.; Goggins M.; Maitra A.; Iacobuzio-Donahue C.; Eshleman J.R.; Kern S.E.; Hruban R.H.; Karchin R.; Papadopoulos N.; Parmigiani G.; Vogelstein B.; Velculescu V.E.; Kinzler K.W.;
Science 321:1801-1806(2008)
Cited for: VARIANT [LARGE SCALE ANALYSIS] THR-880;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q2M3G0: Variant p.Ala880Thr