UniProtKB/SwissProt variant VAR

Variant information

Variant position:

57

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 Asparagine (N) to Serine (S) at position 57 (N57S, p.Asn57Ser).

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 (N) to small size and polar (S)

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:

Loss of higher molecular weight isoform.

Any additional useful information about the variant.

Other resources:

Links to websites of interest for the variant.

Variant rs561439247 [ dbSNP | Ensembl ]

Sequence information

Variant position:

57

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

Protein sequence length:

504

The length of the canonical sequence.

Location on the sequence:

LRKANDQSGRCQYTFSVASP N ESSCPEQSQAMSVIHNLQRD

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                         LRKANDQSG-----------RCQYT------------------------FSVASPNESSCPEQSQAMSV--IHNLQ-------------------------------------RD

                              LRKANDRSG-----------RCQYI----------------

Mouse                         FRKANDRSG-----------RCQYT----------------

Rat                           FRKANDRSG-----------RCQYT----------------

Bovine                        FQKANDRSG-----------RCQYT----------------

Rabbit                        LRKANDRSG-----------RCQYT----------------

Cat                           LRKANDRSG-----------RCQYT----------------

Slime mold                    FNQKNEPEGGKITNYLLEKSRVVFQLKGERNFHIFYQFCRG

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	33 – 504	Myocilin
Chain	33 – 226	Myocilin, N-terminal fragment
Glycosylation	57 – 57	N-linked (GlcNAc...) asparagine

Literature citations

Characterization of rabbit myocilin: implications for human myocilin glycosylation and signal peptide usage.
Shepard A.R.; Jacobson N.; Sui R.; Steely H.T.; Lotery A.J.; Stone E.M.; Clark A.F.;
BMC Genet. 4:5-5(2003)
Cited for: CHARACTERIZATION OF VARIANT SER-57; GLYCOSYLATION; TISSUE SPECIFICITY; SUBCELLULAR LOCATION;

Myocilin analysis by DHPLC in French POAG patients: increased prevalence of Q368X mutation.
Melki R.; Belmouden A.; Brezin A.; Garchon H.-J.;
Hum. Mutat. 22:179-179(2003)
Cited for: VARIANTS GLC1A ARG-367; ILE-438; LYS-480 AND PHE-499; VARIANTS SER-57; LYS-76 AND ARG-398;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q99972: Variant p.Asn57Ser