UniProtKB/SwissProt variant VAR

Variant information

Variant position:

1323

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 Leucine (L) at position 1323 (P1323L, p.Pro1323Leu).

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:

Similar physico-chemical property. Both residues are medium size and hydrophobic.

The physico-chemical property of the reference and variant residues and the change implicated.

BLOSUM score:

-3

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 rs3753841 [ dbSNP | Ensembl ]

Sequence information

Variant position:

1323

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

Protein sequence length:

1806

The length of the canonical sequence.

Location on the sequence:

GPKGNPGPVGFPGDPGPPGE P GPAGQDGVGGDKGEDGDPGQ

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                         GPKGNPGPVGFPGDPGPPGEPGPAGQDGVGGDKGEDGDPGQ

Mouse                         GPKGNPGPVGFPGDPGPPGEPGPAGQDGVGGDKGEDGDPGQ

Rat                           GPKGNPGPVGFPGDPGPPGEPGPAGQDGVGGDKGEDGDPGQ

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	512 – 1563	Collagen alpha-1(XI) chain
Region	527 – 1563	Disordered
Region	529 – 1542	Triple-helical region
Compositional bias	1291 – 1324	Pro residues

Literature citations

Pro-alpha 1(XI) collagen. Structure of the amino-terminal propeptide and expression of the gene in tumor cell lines.
Yoshioka H.; Ramirez F.;
J. Biol. Chem. 265:6423-6426(1990)
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM A); VARIANTS LEU-1323 AND PRO-1535;

Splicing mutations of 54-bp exons in the COL11A1 gene cause Marshall syndrome, but other mutations cause overlapping Marshall/Stickler phenotypes.
Annunen S.; Koerkkoe J.; Czarny M.; Warman M.L.; Brunner H.G.; Kaeaeriaeinen H.; Mulliken J.B.; Tranebjaerg L.; Brooks D.G.; Cox G.F.; Cruysberg J.R.; Curtis M.A.; Davenport S.L.H.; Friedrich C.A.; Kaitila I.; Krawczynski M.R.; Latos-Bielenska A.; Mukai S.; Olsen B.R.; Shinno N.; Somer M.; Vikkula M.; Zlotogora J.; Prockop D.J.; Ala-Kokko L.;
Am. J. Hum. Genet. 65:974-983(1999)
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]; ALTERNATIVE SPLICING (ISOFORMS A; B AND C); VARIANTS STL2/MARSHALL SYNDROME ARG-676; 921-GLN--PRO-926 DEL; 1313-PHE--GLY-1315 DEL; LEU-1323; VAL-1516 AND PRO-1535;

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] (ISOFORM 4); VARIANTS LEU-1323 AND PRO-1535;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot P12107: Variant p.Pro1323Leu