UniProtKB/SwissProt variant VAR

Variant information

Variant position:

1875

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

Type of variant:

LP/P [Disclaimer]

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 1875 (G1875R, p.Gly1875Arg).

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 CMS8.

Any additional useful information about the variant.

Sequence information

Variant position:

1875

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

Protein sequence length:

2068

The length of the canonical sequence.

Location on the sequence:

HCEKGLVEKSAGDVDTLAFD G RTFVEYLNAVTESELANEIP

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                         HCEKGLVEKSAGDVDTLAFDGRTFVEYLNAVTESELANEIP

Mouse                         HCEKGIVEKSVGDLETLAFDGRTYIEYLNAVTESELTNEIP

Rat                           HCEKGLVEKSVGDLETLAFDGRTYIEYLNAVIESELTNEIP

Chicken                       HCEKVIIEKAAGDAEAIAFDGRTYMEYHNAVTKSHLSNEIP

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	30 – 2068	Agrin
Chain	1103 – 2068	Agrin C-terminal 110 kDa subunit
Chain	1864 – 2068	Agrin C-terminal 22 kDa fragment
Domain	1868 – 2065	Laminin G-like 3
Site	1862 – 1862	Critical for cleavage by neurotrypsin
Site	1888 – 1888	Alternative splice site to produce 'z' isoforms
Site	1892 – 1892	Highly important for the agrin receptor complex activity of the 'z(8)' insert

Literature citations

Agrin mutations lead to a congenital myasthenic syndrome with distal muscle weakness and atrophy.
Nicole S.; Chaouch A.; Torbergsen T.; Bauche S.; de Bruyckere E.; Fontenille M.J.; Horn M.A.; van Ghelue M.; Loeseth S.; Issop Y.; Cox D.; Mueller J.S.; Evangelista T.; Staalberg E.; Ioos C.; Barois A.; Brochier G.; Sternberg D.; Fournier E.; Hantai D.; Abicht A.; Dusl M.; Laval S.H.; Griffin H.; Eymard B.; Lochmueller H.;
Brain 137:2429-2443(2014)
Cited for: VARIANT VAL-745; VARIANTS CMS8 SER-76; ILE-105 AND ARG-1875; CHARACTERIZATION OF VARIANTS CMS8 SER-76 AND ILE-105;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot O00468: Variant p.Gly1875Arg