UniProtKB/SwissProt variant VAR

Variant information

Variant position:

2927

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

Type of variant:

Polymorphism

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 Methionine (M) to Threonine (T) at position 2927 (M2927T, p.Met2927Thr).

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 (M) to medium size and polar (T)

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

BLOSUM score:

-1

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

Other resources:

Links to websites of interest for the variant.

Variant rs6728818 [ dbSNP | Ensembl ]

Sequence information

Variant position:

2927

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

Protein sequence length:

3177

The length of the canonical sequence.

Location on the sequence:

PAAAKPAPAKPVAAKPVATK M ATVRPPVAVKPATAAKPVAA

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                         PAAAKPAPAKPVAAKPVATKMATVRPPVAVKPATAAKPVAA

Chicken                       TTTASTTAQTRATERPTESTTVQVNATVQSQGSTAANTKAT

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	26 – 3177	Collagen alpha-3(VI) chain
Region	2376 – 3177	Nonhelical region
Compositional bias	2908 – 2983	Ala-rich
Alternative sequence	1444 – 3177	Missing. In isoform 3 and isoform 5.

Literature citations

Mosaic structure of globular domains in the human type VI collagen alpha 3 chain: similarity to von Willebrand factor, fibronectin, actin, salivary proteins and aprotinin type protease inhibitors.
Chu M.-L.; Zhang R.-Z.; Pan T.-C.; Stokes D.; Conway D.; Kuo H.-J.; Glanville R.; Mayer U.; Mann K.; Deutzmann R.; Timpl R.;
EMBO J. 9:385-393(1990)
Cited for: NUCLEOTIDE SEQUENCE [MRNA]; PARTIAL PROTEIN SEQUENCE; HYDROXYLATION AT PRO-2100; LYS-2103; PRO-2206; LYS-2209; LYS-2212; PRO-2239; PRO-2316; PRO-2319; LYS-2322 AND LYS-2337; VARIANTS VAL-2431; THR-2927; VAL-2988 AND PRO-3012;

UniProtKB/Swiss-Prot P12111: Variant p.Met2927Thr