Home  |  Contact

UniProtKB/Swiss-Prot P02458: Variant p.Gly1170Ser

Collagen alpha-1(II) chain
Gene: COL2A1
Variant information

Variant position:  1170
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 1170 (G1170S, p.Gly1170Ser).
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:  Legg-Calve-Perthes disease (LCPD) [MIM:150600]: Characterized by loss of circulation to the femoral head, resulting in avascular necrosis in a growing child. Clinical pictures of the disease vary, depending on the phase of disease progression through ischemia, revascularization, fracture and collapse, and repair and remodeling of the bone. {ECO:0000269|PubMed:17394019}. 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.

Involvement in disease:  Avascular necrosis of femoral head, primary, 1 (ANFH1) [MIM:608805]: A disease characterized by mechanical failure of the subchondral bone, and degeneration of the hip joint. It usually leads to destruction of the hip joint in the third to fifth decade of life. The clinical manifestations, such as pain on exertion, a limping gait, and a discrepancy in leg length, cause considerable disability. ANFH1 inheritance is autosomal dominant. {ECO:0000269|PubMed:15930420, ECO:0000269|PubMed:21671384}. 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 ANFH1 and LCPD.
Any additional useful information about the variant.

Other resources:  
Links to websites of interest for the variant.



Sequence information

Variant position:  1170
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:  1487
The length of the canonical sequence.

Location on the sequence:   DQGASGPAGPSGPRGPPGPV  G PSGKDGANGIPGPIGPPGPR
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                         DQGASGPAGPSGPRGPPGPVGPSGKDGANGIPGPIGPPGPR

Mouse                         DQGASGPAGPSGPRGPPGPVGPSGKDGSNGIPGPIGPPGPR

Rat                           DQGTSGPAGPSGPRGPPGPVGPSGKDGSNGIPGPIGPPGPR

Bovine                        DQGASGPAGPSGPRGPPGPVGPSGKDGANGIPGPIGPPGPR

Xenopus laevis                DQGATGPAGPAGPRGPPGPVGPSGKDGSNGISGPIGPPGPR

Xenopus tropicalis            DQGASGPAGPGGPRGPPGPVGPSGKDGSNGLPGPIGPPGPR

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 182 – 1241 Collagen alpha-1(II) chain
Region 201 – 1214 Triple-helical region
Modified residue 1181 – 1181 4-hydroxyproline
Modified residue 1186 – 1186 3-hydroxyproline
Modified residue 1187 – 1187 4-hydroxyproline
Alternative sequence 1 – 1219 Missing. In isoform 3.


Literature citations

Type II collagen gene variants and inherited osteonecrosis of the femoral head.
Liu Y.-F.; Chen W.-M.; Lin Y.-F.; Yang R.-C.; Lin M.-W.; Li L.-H.; Chang Y.-H.; Jou Y.-S.; Lin P.-Y.; Su J.-S.; Huang S.-F.; Hsiao K.-J.; Fann C.S.J.; Hwang H.-W.; Chen Y.-T.; Tsai S.-F.;
N. Engl. J. Med. 352:2294-2301(2005)
Cited for: VARIANTS ANFH1 SER-717 AND SER-1170;

A recurrent mutation in type II collagen gene causes Legg-Calve-Perthes disease in a Japanese family.
Miyamoto Y.; Matsuda T.; Kitoh H.; Haga N.; Ohashi H.; Nishimura G.; Ikegawa S.;
Hum. Genet. 121:625-629(2007)
Cited for: VARIANT LCPD SER-1170;

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.