UniProtKB/SwissProt variant VAR

Variant information

Variant position:

560

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

Type of variant:

LP/P [Disclaimer]

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 Glycine (G) to Serine (S) at position 560 (G560S, p.Gly560Ser).

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 small size and polar (S)

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 OI4.

Any additional useful information about the variant.

Other resources:

Links to websites of interest for the variant.

Variant rs67507747 [ dbSNP | Ensembl ]

Sequence information

Variant position:

560

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

Protein sequence length:

1464

The length of the canonical sequence.

Location on the sequence:

LTGSPGSPGPDGKTGPPGPA G QDGRPGPPGPPGARGQAGVM

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                         LTGSPGSPGPDGKTGPPGPAGQDGRPGPPGPPGARGQAGVM

                              LTGSPGSPGPDGKTGPPGPAGQDGRPGPPGPPGARGQAGVM

Mouse                         LTGSPGSPGPDGKTGPPGPAGQDGRPGPAGPPGARGQAGVM

Rat                           LTGSPGSPGPDGKTGPPGPAGQDGRPGPAGPPGARGQAGVM

Bovine                        LTGSPGSPGPDGKTGPPGPAGQDGRPGPPGPPGARGQAGVM

Chicken                       LTGSPGSPGPDGKTGPPGPAGQDGRPGPAGPPGARGQAGVM

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	162 – 1218	Collagen alpha-1(I) chain
Region	179 – 1192	Triple-helical region
Modified residue	544 – 544	4-hydroxyproline
Modified residue	547 – 547	4-hydroxyproline
Modified residue	556 – 556	4-hydroxyproline
Modified residue	565 – 565	4-hydroxyproline
Modified residue	571 – 571	4-hydroxyproline

Literature citations

An RT-PCR-SSCP screening strategy for detection of mutations in the gene encoding the alpha 1 chain of type I collagen: application to four patients with osteogenesis imperfecta.
Mackay K.; Byers P.H.; Dalgleish R.;
Hum. Mol. Genet. 2:1155-1160(1993)
Cited for: VARIANTS OI2 SER-425 AND SER-530; VARIANT OI4 SER-560; VARIANT OI3 SER-719; VARIANT ALA-823;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot P02452: Variant p.Gly560Ser