UniProtKB/Swiss-Prot Q7Z408: Variant p.Met2554Val

• Variant information
• Sequence information
• Literature citations
• All

Variant information

Variant position: 2554 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 Methionine (M) to Valine (V) at position 2554 (M2554V, p.Met2554Val). 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: 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 rs2641962 [ dbSNP | Ensembl ]

Sequence information

Variant position: 2554 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length: 3487 The length of the canonical sequence.
Location on the sequence: PEAPKNGMVFGKEYTVGTKA M YSCSEGYHLQAGAEATAECL 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.
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	1 – 3487	CUB and sushi domain-containing protein 2
Topological domain	1 – 3408	Extracellular
Domain	2529 – 2590	Sushi 15
Disulfide bond	2531 – 2573
Alternative sequence	578 – 3487	Missing. In isoform 3.
Alternative sequence	2297 – 3487	Missing. In isoform 2.

Literature citations

Comparative analysis of CSMD families.
Shimizu A.; Sasaki T.; Asakawa S.; Shimizu N.;
Cited for: NUCLEOTIDE SEQUENCE (ISOFORM 4); VARIANT VAL-2554;