Home  |  Contact

UniProtKB/Swiss-Prot Q9NZR4: Variant p.Gly239Arg

Visual system homeobox 1
Gene: VSX1
Variant information

Variant position:  239
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Type of variant:  US
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 239 (G239R, p.Gly239Arg).
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 KTCN1; unknown pathological significance.
Any additional useful information about the variant.

Other resources:  
Links to websites of interest for the variant.



Sequence information

Variant position:  239
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:  365
The length of the canonical sequence.

Location on the sequence:   WRKREKRWGGSSVMAEYGLY  G AMVRHCIPLPDSVLNSAEGG
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                         WRKREKRWGGSSVMAEYGLYGAMVRHCIPLPDSVLNSAEGG

Mouse                         WRKREKRWGGSSVMAEYGLYGAMVRHCIPLPDSVLNSADS-

Bovine                        WRKREKRWGGSSVMAEYGLYGAMVRHCIPLPDSVLGSGEGG

Chicken                       WRKREKCWGRSSVMAEYGLYGAMVRHSIPLPESIINSAKSG

Xenopus laevis                WRKREKCWGRSSVMAEYGLYGAMVRHSIPLPESIINSAKNG

Zebrafish                     WRKREKCWGRSSVMAEYGLYGAMVRHSIPLPESIINSAKSG

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.

TypePositionsDescription
Chain 1 – 365 Visual system homeobox 1
Domain 224 – 277 CVC
Alternative sequence 144 – 365 Missing. In isoform 4.
Alternative sequence 211 – 239 WFQNRRAKWRKREKRWGGSSVMAEYGLYG -> SGVPFLRSKDTTENVSFPHSVSQSAVPSL. In isoform 2 and isoform 3.
Alternative sequence 219 – 365 Missing. In isoform 6.
Alternative sequence 237 – 365 Missing. In isoform 7.


Literature citations

Mutational screening of VSX1, SPARC, SOD1, LOX, and TIMP3 in keratoconus.
De Bonis P.; Laborante A.; Pizzicoli C.; Stallone R.; Barbano R.; Longo C.; Mazzilli E.; Zelante L.; Bisceglia L.;
Mol. Vis. 17:2482-2494(2011)
Cited for: VARIANTS KTCN1 PRO-17; ASP-160; ARG-239 AND ARG-247; VARIANT GLU-144;

Disclaimer: Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. They are not in any way intended to be used as a substitute for professional medical advice, diagnostic, treatment or care.