UniProtKB/SwissProt variant VAR

Variant information

Variant position:

445

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 Alanine (A) to Valine (V) at position 445 (A445V, p.Ala445Val).

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 small size and hydrophobic (A) to medium size and hydrophobic (V)

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

BLOSUM score:

0

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 GLC1A; no effect on protein stability.

Any additional useful information about the variant.

Other resources:

Links to websites of interest for the variant.

Variant rs140967767 [ dbSNP | Ensembl ]

Sequence information

Variant position:

445

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:

SVANAFIICGTLYTVSSYTS A DATVNFAYDTGTGISKTLTI

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                         SVA---------NAFIICGTLYTVSSYTSADATVNFAYDTGTG------------------------------------ISKTLTI

                              SVA---------NAFVICGHLYTISSYSSPDATVNFAYDTG

Mouse                         SVA---------NAFVICGILYTVSSYSSAHATVNFAYDTK

Rat                           SVA---------NAFVICGILYTVSSYSSVHATINFAYDTN

Bovine                        SVA---------NAFIICGTLYTVSSYSSPDATVNFAYDTG

Rabbit                        SVA---------NAFIICGTLYTVSSYSSADATVNFAYDTG

Cat                           SVA---------NAFIICGRLYTVSSYSAPDATINFAYDTG

Slime mold                    APAPGGAPMMKKPAPVPGGPAPGGSAIMKPAGGVSKPLPSP

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	227 – 504	Myocilin, C-terminal fragment
Domain	244 – 503	Olfactomedin-like
Metal binding	428 – 428	Calcium
Metal binding	429 – 429	Calcium; via carbonyl oxygen
Beta strand	435 – 445

Literature citations

Structural basis for misfolding in myocilin-associated glaucoma.
Donegan R.K.; Hill S.E.; Freeman D.M.; Nguyen E.; Orwig S.D.; Turnage K.C.; Lieberman R.L.;
Hum. Mol. Genet. 24:2111-2124(2015)
Cited for: X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS) OF 228-504 IN COMPLEX WITH CALCIUM; DISULFIDE BONDS; CHARACTERIZATION OF VARIANTS GLC1A LYS-293; ILE-353 AND VAL-445; CHARACTERIZATION OF VARIANTS MET-329; CYS-422; PRO-425 AND CYS-473;

Digenic inheritance of early-onset glaucoma: CYP1B1, a potential modifier gene.
Vincent A.L.; Billingsley G.; Buys Y.; Levin A.V.; Priston M.; Trope G.; Williams-Lyn D.; Heon E.;
Am. J. Hum. Genet. 70:448-460(2002)
Cited for: VARIANTS GLC1A ARG-252; LYS-293; ARG-367; LEU-370; LYS-377; VAL-399 AND VAL-445; VARIANT ARG-398;

Founder TIGR/myocilin mutations for glaucoma in the Quebec population.
Faucher M.; Anctil J.-L.; Rodrigue M.-A.; Duchesne A.; Bergeron D.; Blondeau P.; Cote G.; Dubois S.; Bergeron J.; Arseneault R.; Morissette J.; Raymond V.;
Hum. Mol. Genet. 11:2077-2090(2002)
Cited for: VARIANTS GLC1A TRP-126; LYS-293; LYS-352; ARG-367; GLU-423; THR-427; VAL-445 AND LEU-481; VARIANTS LYS-76; GLU-77 AND ARG-398;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q99972: Variant p.Ala445Val