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UniProtKB/Swiss-Prot P02458: Variant p.Thr1390Asn

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

Variant position:  1390
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 Threonine (T) to Asparagine (N) at position 1390 (T1390N, p.Thr1390Asn).
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:  Similar physico-chemical property. Both residues are medium size and polar.
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 PLSD-T; phenotype previously considered as achondrogenesis-hypochondrogenesis type 2.
Any additional useful information about the variant.



Sequence information

Variant position:  1390
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:   TANVQMTFLRLLSTEGSQNI  T YHCKNSIAYLDEAAGNLKKA
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                         TANVQMTFLRLLSTEGSQNITYHCKNSIAYLDEAAGNLKKA

Mouse                         TANVQMTFLRLLSTEGSQNITYHCKNSIAYLDEAAGNLKKA

Rat                           TANVQMTFLRLLSTEGSQNITYHCKNSIAYLDEAAGNLKKA

Bovine                        TANVQMTFLRLLSTEGSQNITYHCKNSIAYLDEAAGNLKKA

Xenopus laevis                TANIQMTFLRLLSTDASQNITYHCKNSIAFMDEASGNLKKA

Xenopus tropicalis            TANIQMTFLRLLSTDATQNITYHCKNSIAFMDEASGNLKKA

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

Report of five novel and one recurrent COL2A1 mutations with analysis of genotype-phenotype correlation in patients with a lethal type II collagen disorder.
Mortier G.R.; Weis M.; Nuytinck L.; King L.M.; Wilkin D.J.; De Paepe A.; Lachman R.S.; Rimoin D.L.; Eyre D.R.; Cohn D.H.;
J. Med. Genet. 37:263-271(2000)
Cited for: VARIANTS ACG2 SER-513; VAL-717; ALA-771; CYS-1110 AND SER-1143; VARIANT PLSD-T ASN-1390;

Dominant negative mutations in the C-propeptide of COL2A1 cause platyspondylic lethal skeletal dysplasia, torrance type, and define a novel subfamily within the type 2 collagenopathies.
Zankl A.; Neumann L.; Ignatius J.; Nikkels P.; Schrander-Stumpel C.; Mortier G.; Omran H.; Wright M.; Hilbert K.; Bonafe L.; Spranger J.; Zabel B.; Superti-Furga A.;
Am. J. Med. Genet. A 133:61-67(2005)
Cited for: VARIANTS PLSD-T PRO-1448; HIS-1469; VAL-1484 DEL AND GLY-1485; DISCUSSION OF VARIANT ASN-1390;

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.