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UniProtKB/Swiss-Prot P02458: Variant p.Thr9Ser

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

Variant position:  9
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Type of variant:  LB/B
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 Serine (S) at position 9 (T9S, p.Thr9Ser).
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 medium size and polar (T) to small size and polar (S)
The physico-chemical property of the reference and variant residues and the change implicated.

BLOSUM score:  1
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

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



Sequence information

Variant position:  9
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:   MIRLGAPQ  T LVLLTLLVAAVLRCQGQDVQ
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                         MIRLGAPQTLVLLT---LLVAAVLRCQGQ-DVQ

Mouse                         MIRLGAPQSLVLLT---LLIAAVLRCQGQ

Rat                           MIRLGAPQSLVLLT---LLIATVLQCQGQ

Bovine                        MIRLGAPQTLVLLT---LLVAAVLRCHGQ

Xenopus laevis                MFSFVDSRTLVLFAATQVILLAVVRCQDE

Xenopus tropicalis            MFSFVDSRTLVLFAATQVILLAVVRCQDE

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
Signal peptide 1 – 25
Alternative sequence 1 – 1219 Missing. In isoform 3.


Literature citations

Nucleotide sequence of the full length cDNA encoding for human type II procollagen.
Su M.W.; Lee B.; Ramirez F.; Machado M.A.; Horton W.A.;
Nucleic Acids Res. 17:9473-9473(1989)
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1); VARIANTS SER-9 AND LEU-158;

Conservation of the sizes of 53 introns and over 100 intronic sequences for the binding of common transcription factors in the human and mouse genes for type II procollagen (COL2A1).
Ala-Kokko L.; Kvist A.-P.; Metsaranta M.; Kivirikko K.I.; de Crombrugghe B.; Prockop D.J.; Vuorio E.;
Biochem. J. 308:923-929(1995)
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (ISOFORM 2); VARIANT SER-9;

Structure of cDNA clones coding for human type II procollagen. The alpha 1(II) chain is more similar to the alpha 1(I) chain than two other alpha chains of fibrillar collagens.
Baldwin C.T.; Reginato A.M.; Smith C.; Jimenez S.A.; Prockop D.J.;
Biochem. J. 262:521-528(1989)
Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 1-1229 (ISOFORM 1); VARIANT SER-9;

Organization of the exons coding for pro alpha 1(II) collagen N-propeptide confirms a distinct evolutionary history of this domain of the fibrillar collagen genes.
Su M.W.; Benson-Chanda V.; Vissing H.; Ramirez F.;
Genomics 4:438-441(1989)
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-236 (ISOFORM 1); VARIANT SER-9;

The human type II procollagen gene: identification of an additional protein-coding domain and location of potential regulatory sequences in the promoter and first intron.
Ryan M.C.; Sieraski M.; Sandell L.J.;
Genomics 8:41-48(1990)
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-103 (ISOFORM 2); VARIANT SER-9;

A COL2A1 mutation in achondrogenesis type II results in the replacement of type II collagen by type I and III collagens in cartilage.
Chan D.; Cole W.G.; Chow C.W.; Mundlos S.; Bateman J.F.;
J. Biol. Chem. 270:1747-1753(1995)
Cited for: VARIANT ACG2 SER-969;

Widely distributed mutations in the COL2A1 gene produce achondrogenesis type II/hypochondrogenesis.
Koerkkoe J.; Cohn D.H.; Ala-Kokko L.; Krakow D.; Prockop D.J.;
Am. J. Med. Genet. 92:95-100(2000)
Cited for: VARIANTS ACG2 VAL-453; ASP-453; ASP-771; ARG-780; ARG-795; GLU-894; ASP-948; SER-981; VAL-1065 AND ARG-1119; VARIANT HYPOCHONDROGENESIS 1017-GLY--VAL-1022 DEL; VARIANT ILE-1331;

Natural variation in four human collagen genes across an ethnically diverse population.
Chan T.F.; Poon A.; Basu A.; Addleman N.R.; Chen J.; Phong A.; Byers P.H.; Klein T.E.; Kwok P.Y.;
Genomics 91:307-314(2008)
Cited for: VARIANTS SER-9; ASP-142; ILE-638; THR-1051; ILE-1331 AND SER-1405;

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.