Home  |  Contact

UniProtKB/Swiss-Prot P02458: Variant p.Tyr1391Cys

Collagen alpha-1(II) chain
Gene: COL2A1
Chromosomal location: 12q13.11-q13.2
Variant information

Variant position:  1391
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 Tyrosine (Y) to Cysteine (C) at position 1391 (Y1391C, p.Tyr1391Cys).
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 large size and aromatic (Y) to medium size and polar (C)
The physico-chemical property of the reference and variant residues and the change implicated.

BLOSUM score:  -2
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:  Platyspondylic lethal skeletal dysplasia Torrance type (PLSD-T) [MIM:151210]: Platyspondylic lethal skeletal dysplasias (PLSDs) are a heterogeneous group of chondrodysplasias characterized by severe platyspondyly and limb shortening. PLSD-T is characterized by varying platyspondyly, short ribs with anterior cupping, hypoplasia of the lower ilia with broad ischial and pubic bones, and shortening of the tubular bones with splayed and cupped metaphyses. Histology of the growth plate typically shows focal hypercellularity with slightly enlarged chondrocytes in the resting cartilage and relatively well-preserved columnar formation and ossification at the chondro-osseous junction. PLSD-T is generally a perinatally lethal disease, but a few long-term survivors have been reported. {ECO:0000269|PubMed:10745044, ECO:0000269|PubMed:14729840, ECO:0000269|PubMed:15643621}. 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 PLSD-T.
Any additional useful information about the variant.

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



Sequence information

Variant position:  1391
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:   ANVQMTFLRLLSTEGSQNIT  Y HCKNSIAYLDEAAGNLKKAL
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                         ANVQMTFLRLLSTEGSQNITYHCKNSIAYLDEAAGNLKKAL

Mouse                         ANVQMTFLRLLSTEGSQNITYHCKNSIAYLDEAAGNLKKAL

Rat                           ANVQMTFLRLLSTEGSQNITYHCKNSIAYLDEAAGNLKKAL

Bovine                        ANVQMTFLRLLSTEGSQNITYHCKNSIAYLDEAAGNLKKAL

Xenopus laevis                ANIQMTFLRLLSTDASQNITYHCKNSIAFMDEASGNLKKAV

Xenopus tropicalis            ANIQMTFLRLLSTDATQNITYHCKNSIAFMDEASGNLKKAV

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 1242 – 1487 Chondrocalcin
Domain 1253 – 1487 Fibrillar collagen NC1
Glycosylation 1388 – 1388 N-linked (GlcNAc...) asparagine
Disulfide bond 1323 – 1485


Literature citations

Identification of COL2A1 mutations in platyspondylic skeletal dysplasia, Torrance type.
Nishimura G.; Nakashima E.; Mabuchi A.; Shimamoto K.; Shimamoto T.; Shimao Y.; Nagai T.; Yamaguchi T.; Kosaki R.; Ohashi H.; Makita Y.; Ikegawa S.;
J. Med. Genet. 41:75-79(2004)
Cited for: VARIANT PLSD-T CYS-1391;

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.