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UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot P02458: Variant p.Gly909Cys

Collagen alpha-1(II) chain
Gene: COL2A1
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Variant information Variant position: help 909 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Type of variant: help 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: help From Glycine (G) to Cysteine (C) at position 909 (G909C, p.Gly909Cys). 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: help Change from glycine (G) to medium size and polar (C) The physico-chemical property of the reference and variant residues and the change implicated.
BLOSUM score: help -3 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: help In SEMDSTWK. Any additional useful information about the variant.
Other resources: help Links to websites of interest for the variant.


Sequence information Variant position: help 909 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length: help 1487 The length of the canonical sequence.
Location on the sequence: help AQGPPGATGFPGAAGRVGPP G SNGNPGPPGPPGPSGKDGPK 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: help The multiple alignment of the region surrounding the variant against various orthologous sequences. 
Human                         AQGPPGATGFPGAAGRVGPPGSNGNPGPPGPPGPSGKDGPK

Mouse                         AQGPPGATGFPGAAGRVGPPGANGNPGPAGPPGPAGKDGPK

Rat                           AQGPPGATGFPGAAGRVGPPGSNGNPGPAGPPGPAGKDGPK

Bovine                        AQGPPGATGFPGAAGRVGPPGSNGNPGPPGPPGPSGKDGPK

Xenopus laevis                AQGPAGATGFPGAAGRVGTPGPNGNPGPPGPPGSAGKEGPK

Xenopus tropicalis            AQGPPGATGFPGAAGRVGPPGPNGNPGPSGAPGSAGKEGPK
Sequence annotation in neighborhood: help 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 97 – 1237 Disordered
Region 201 – 1214 Triple-helical region
Modified residue 907 – 907 3-hydroxyproline
Modified residue 908 – 908 4-hydroxyproline
Modified residue 914 – 914 4-hydroxyproline
Modified residue 920 – 920 4-hydroxyproline
Alternative sequence 1 – 1219 Missing. In isoform 3.



Literature citations
A dominant mutation in the type II collagen gene (COL2A1) produces spondyloepimetaphyseal dysplasia (SEMD), Strudwick type.
Tiller G.E.; Weis M.A.; Lachman R.S.; Cohn D.H.; Rimoin D.L.; Eyre D.R.;
Cited for: VARIANTS SEMDSTWK VAL-897 AND CYS-909; Dominant mutations in the type II collagen gene, COL2A1, produce spondyloepimetaphyseal dysplasia, Strudwick type.
Tiller G.E.; Polumbo P.A.; Weis M.A.; Bogaert R.; Lachman R.S.; Cohn D.H.; Rimoin D.L.; Eyre D.R.;
Nat. Genet. 11:87-89(1995)
Cited for: VARIANTS SEMDSTWK VAL-492; CYS-504 AND CYS-909;
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.