UniProtKB/Swiss-Prot P08123: Variant p.Pro549Ala

Collagen alpha-2(I) chain
Gene: COL1A2
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Variant information Variant position:

549 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 Proline (P) to Alanine (A) at position 549 (P549A, p.Pro549Ala). 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 hydrophobic (P) to small size and hydrophobic (A) 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.

Variant rs42524 [ dbSNP | Ensembl ]

Sequence information Variant position:

549 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length:

1366 The length of the canonical sequence.
Location on the sequence:

GAQGPPGPQGVQGGKGEQGP P GPPGFQGLPGPSGPAGEVGK 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                         GAQGPPGPQGVQGGKGEQGPPGPPGFQGLPGPSGPAGEVGK

                              GAQGPPGPQGVQGGKGEQGPAGPPGFQGLPGPAGTAGEVGK

Mouse                         GAQGPPGPQGVQGGKGEQGPAGPPGFQGLPGPSGTTGEVGK

Rat                           GAQGPPGPQGVQGGKGEQGPAGPPGFQGLPGPSGTAGEVGK

Bovine                        GAQGPPGLQGVQGGKGEQGPAGPPGFQGLPGPAGTAGEAGK

Chicken                       GAQGPPGVTGNQGAKGETGPAGPPGFQGLPGPSGPAGEAGK

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.

Type	Positions	Description
Chain	80 – 1119	Collagen alpha-2(I) chain
Region	28 – 1130	Disordered

Literature citations
Organization of the human pro-alpha 2(I) collagen gene.
de Wet W.J.; Bernard M.P.; Benson-Chanda V.; Chu M.-L.; Dickson L.A.; Weil D.; Ramirez F.;
J. Biol. Chem. 262:16032-16036(1987)
Cited for: NUCLEOTIDE SEQUENCE [MRNA]; VARIANTS ASN-249; THR-276; VAL-483; ALA-549; HIS-678; GLY-743; PHE-1022; GLU-1189; PRO-1198 AND HIS-1354; The human type I collagen mutation database.
Dalgleish R.;
Nucleic Acids Res. 25:181-187(1997)
Cited for: NUCLEOTIDE SEQUENCE [MRNA]; REVIEW ON OI VARIANTS; VARIANTS ALA-549; HIS-678 AND HIS-1354; The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).
The MGC Project Team;
Genome Res. 14:2121-2127(2004)
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]; VARIANT ALA-549; Single base mutation in the pro alpha 2(I) collagen gene that causes efficient splicing of RNA from exon 27 to exon 29 and synthesis of a shortened but in-frame pro alpha 2(I) chain.
Tromp G.; Prockop D.J.;
Proc. Natl. Acad. Sci. U.S.A. 85:5254-5258(1988)
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 520-573; VARIANT ALA-549; Chemical cleavage method for the detection of RNA base changes: experience in the application to collagen mutations in osteogenesis imperfecta.
Bateman J.F.; Lamande S.R.; Hannagan M.; Moeller I.; Dahl H.-H.M.; Cole W.G.;
Am. J. Med. Genet. 45:233-240(1993)
Cited for: VARIANT ALA-549; 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-528; ALA-549 AND THR-564; Mutation and polymorphism spectrum in osteogenesis imperfecta type II: implications for genotype-phenotype relationships.
Bodian D.L.; Chan T.F.; Poon A.; Schwarze U.; Yang K.; Byers P.H.; Kwok P.Y.; Klein T.E.;
Hum. Mol. Genet. 18:463-471(2009)
Cited for: VARIANTS OI2 CYS-234; ARG-283; GLU-397; CYS-454; LEU-457; 461-PRO--GLY-466 DEL; GLU-526; VAL-562; 705-ALA--PRO-707 DEL; ARG-739; VAL-748; ASP-790; PRO-798 INS; 806-PRO--GLY-811 DEL; VAL-856; SER-949; ASP-955; GLU-1027 AND 1058-PRO--ALA-1062 DEL; VARIANT ALA-549;

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