UniProtKB/SwissProt variant VAR

Variant information

Variant position:

279

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 279 (Q279R, p.Gln279Arg).

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

Variant description:

May be associated with susceptibility to IDD.

Any additional useful information about the variant.

Other resources:

Links to websites of interest for the variant.

Variant rs17576 [ dbSNP | Ensembl ]

Sequence information

Variant position:

279

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

Protein sequence length:

707

The length of the canonical sequence.

Location on the sequence:

TANYDTDDRFGFCPSERLYT Q DGNADGKPCQFPFIFQGQSY

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                         TANYDTDDRFGFCPSERLYTQDGNADGKPCQFPFIFQGQSY

                              TADYDTDRRFGFCPSEKLYAQDGNGDGKPCVFPFTFEGRSY

Mouse                         TADYDKDGKFGFCPSERLYTEHGNGEGKPCVFPFIFEGRSY

Rat                           TADYDTDRKYGFCPSENLYTEHGNGDGKPCVFPFIFEGHSY

Bovine                        TADYDADRQFGFCPSERLYTQDGNADGKPCVFPFTFQGRTY

Rabbit                        TADYDTDRRFGFCPSERLYTQDGNADGKPCEFPFIFQGRTY

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	107 – 707	82 kDa matrix metalloproteinase-9
Beta strand	279 – 283

Literature citations

SV40-transformed human lung fibroblasts secrete a 92-kDa type IV collagenase which is identical to that secreted by normal human macrophages.
Wilhelm S.M.; Collier I.E.; Marmer B.L.; Eisen A.Z.; Grant G.A.; Goldberg G.I.;
J. Biol. Chem. 264:17213-17221(1989)
Cited for: NUCLEOTIDE SEQUENCE [MRNA]; FUNCTION; PROTEIN SEQUENCE OF 20-37; SUBCELLULAR LOCATION; VARIANTS ARG-279 AND PRO-574;

Submission
SeattleSNPs variation discovery resource;
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]; VARIANTS VAL-20; LYS-127; ARG-279; PRO-574 AND GLN-668;

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]; VARIANTS ARG-279 AND PRO-574;

Genetic variation at the matrix metalloproteinase-9 locus on chromosome 20q12.2-13.1.
Zhang B.; Henney A.; Eriksson P.; Hamsten A.; Watkins H.; Ye S.;
Hum. Genet. 105:418-423(1999)
Cited for: VARIANTS VAL-20; LYS-82 AND ARG-279;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot P14780: Variant p.Gln279Arg