UniProtKB/SwissProt variant VAR

Variant information

Variant position:

2500

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 Glutamine (Q) to Arginine (R) at position 2500 (Q2500R, p.Gln2500Arg).

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 (Q) to large size and basic (R)

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 rs1126823 [ dbSNP | Ensembl ]

Sequence information

Variant position:

2500

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

Protein sequence length:

2530

The length of the canonical sequence.

Location on the sequence:

FVQRHMPTIRCQPSGHWEEP Q ITCTDPTTYKRRLQKRSSRH

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                         FVQRHMPTIRCQPSGHWEEPQITCTDPTTYKRRLQKRSSRH

                              FVQRHVPTIRCQPSGHWEKPRITCTDPSTYKRRLQKRSSRA

Mouse                         FVQRHVPTIRCQPSGHWEEPRITCTDPNTYKHRLQKRSMRP

Rat                           FVQRHVPTIRCQPSADWEEPRITCTDPNTYKHRLQKRTMRP

Bovine                        FIQGHVPTIRCQPSGHWEEPRITCTDPATYKRRLQKRSSRP

Chicken                       YIQRHVPTIRCQPNGHWEEPRISCTNPSSYQRRLYKRSPRS

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	17 – 2530	Aggrecan core protein
Chain	393 – 2530	Aggrecan core protein 2
Domain	2445 – 2505	Sushi
Region	2278 – 2530	G3
Disulfide bond	2476 – 2503
Alternative sequence	2445 – 2506	VACGEPPVVEHARTFGQKKDRYEINSLVRYQCTEGFVQRHMPTIRCQPSGHWEEPQITCTDP -> A. In isoform 3.

Literature citations

Age-related changes in the content of the C-terminal region of aggrecan in human articular cartilage.
Dudhia J.; Davidson C.M.; Wells T.M.; Vynios D.H.; Hardingham T.E.; Bayliss M.T.;
Biochem. J. 313:933-940(1996)
Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 1893-2530 (ISOFORM 2); VARIANTS VAL-2079 AND ARG-2500;

A new epidermal growth factor-like domain in the human core protein for the large cartilage-specific proteoglycan. Evidence for alternative splicing of the domain.
Baldwin C.T.; Reginato A.M.; Prockop D.J.;
J. Biol. Chem. 264:15747-15750(1989)
Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 2051-2530 (ISOFORM 1); VARIANTS VAL-2079 AND ARG-2500;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot P16112: Variant p.Gln2500Arg