UniProtKB/Swiss-Prot P02458: Variant p.Gly354Arg

Collagen alpha-1(II) chain
Gene: COL2A1
Feedback?

Variant information Variant position:

354 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 Glycine (G) to Arginine (R) at position 354 (G354R, p.Gly354Arg). 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 glycine (G) to large size and basic (R) 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
Variant description:

In spondylometaphyseal dysplasia; congenital type. Any additional useful information about the variant.
Other resources:

Links to websites of interest for the variant.

Variant rs121912871 [ dbSNP | Ensembl ]

Sequence information Variant position:

354 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:

RTGPAGAAGARGNDGQPGPA G PPGPVGPAGGPGFPGAPGAK 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                         RTGPAGAAGARGNDGQPGPAGPPGPVGPAGGPGFPGAPGAK

Mouse                         RTGPAGAAGARGNDGQPGPAGPPGPVGPAGGPGFPGAPGAK

Rat                           RTGPAGAAGARGNDGQPGPAGPPGPVGPAGGPGFLGAPGAK

Bovine                        RTGPAGAAGARGNDGQPGPAGPPGPVGPAGGPGFPGAPGAK

Xenopus laevis                RPGSSGAAGARGNDGLPGPAGPPGPVGPAGAPGFPGAPGSK

Xenopus tropicalis            RPGASGAAGARGNDGLPGPAGPPGPVGPAGAPGFPGAPGSK

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	182 – 1241	Collagen alpha-1(II) chain
Region	97 – 1237	Disordered
Region	201 – 1214	Triple-helical region
Compositional bias	351 – 365	Pro residues
Modified residue	374 – 374	5-hydroxylysine
Glycosylation	374 – 374	O-linked (Gal...) hydroxylysine
Alternative sequence	1 – 1219	Missing. In isoform 3.

Literature citations
A mutation in the amino-terminal end of the triple helix of type II collagen causing severe osteochondrodysplasia.
Vikkula M.; Ritvaniemi P.; Vuorio A.F.; Kaitila I.; Ala-Kokko L.; Peltonen L.;
Genomics 16:282-285(1993)
Cited for: VARIANT SPONDYLOMETAPHYSEAL DYSPLASIA ARG-354;

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.