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UniProtKB/Swiss-Prot P02452: Variant p.Gly560Ser

Collagen alpha-1(I) chain
Gene: COL1A1
Chromosomal location: 17q21.3-q22
Variant information

Variant position:  560
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 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

Involvement in disease:  Osteogenesis imperfecta 4 (OI4) [MIM:166220]: An autosomal dominant form of osteogenesis imperfecta, a connective tissue disorder characterized by low bone mass, bone fragility and susceptibility to fractures after minimal trauma. Disease severity ranges from very mild forms without fractures to intrauterine fractures and perinatal lethality. Extraskeletal manifestations, which affect a variable number of patients, are dentinogenesis imperfecta, hearing loss, and blue sclerae. OI4 is characterized by moderately short stature, mild to moderate scoliosis, grayish or white sclera and dentinogenesis imperfecta. {ECO:0000269|PubMed:16786509, ECO:0000269|PubMed:16879195, ECO:0000269|PubMed:1770532, ECO:0000269|PubMed:17875077, ECO:0000269|PubMed:1988452, ECO:0000269|PubMed:2745420, ECO:0000269|PubMed:7691343, ECO:0000269|PubMed:7982948, ECO:0000269|PubMed:8094076, ECO:0000269|PubMed:8339541, ECO:0000269|PubMed:9600458}. 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 OI4.
Any additional useful information about the variant.



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.

TypePositionsDescription
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;

Disclaimer: Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. They are not in any way intended to be used as a substitute for professional medical advice, diagnostic, treatment or care.