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UniProtKB/Swiss-Prot O43186: Variant p.Arg41Trp

Cone-rod homeobox protein
Gene: CRX
Chromosomal location: 19q13.3
Variant information

Variant position:  41
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Type of variant:  Disease [Disclaimer]
The variants are classified into three categories: Disease, Polymorphism and Unclassified.
  • Disease: Variants implicated in disease according to literature reports.
  • Polymorphism: Variants not reported to be implicated in disease.
  • Unclassified: Variants with uncertain implication in disease according to literature reports. Evidence against or in favor of a pathogenic role is limited and/or conflicting.

Residue change:  From Arginine (R) to Tryptophan (W) at position 41 (R41W, p.Arg41Trp).
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 large size and basic (R) to large size and aromatic (W)
The physico-chemical property of the reference and variant residues and the change implicated.

BLOSUM score:  -3
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

Involvement in disease:  Cone-rod dystrophy 2 (CORD2) [MIM:120970]: An inherited retinal dystrophy characterized by retinal pigment deposits visible on fundus examination, predominantly in the macular region, and initial loss of cone photoreceptors followed by rod degeneration. This leads to decreased visual acuity and sensitivity in the central visual field, followed by loss of peripheral vision. Severe loss of vision occurs earlier than in retinitis pigmentosa, due to cone photoreceptors degenerating at a higher rate than rod photoreceptors. {ECO:0000269|PubMed:10887186, ECO:0000269|PubMed:9390563, ECO:0000269|PubMed:9427255, ECO:0000269|PubMed:9792858}. Note=The disease is caused by mutations affecting the gene represented in this entry.
The name and a short description of the disease associated with the variant. For more information about the disease, the user can refer to OMIM, following the link provided after the disease acronym.

Variant description:  In CORD2; exhibits reduced DNA binding, transcriptional synergy and interaction with NRL.
Any additional useful information about the variant.

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



Sequence information

Variant position:  41
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:  299
The length of the canonical sequence.

Location on the sequence:   PSVDLMHQAVPYPSAPRKQR  R ERTTFTRSQLEELEALFAKT
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                         PSVDLMHQAVPYPSAPRKQRRERTTFTRSQLEELEALFAKT

                              PSVDLMHQAVSYPSAPRKQRRERTTFTRSQLEELEALFAKT

Mouse                         PNVDLMHQAVPYSSAPRKQRRERTTFTRSQLEELEALFAKT

Bovine                        PSVDLMHPAVSYPSAPRKQRRERTTFTRSQLEELEALFAKT

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 – 299 Cone-rod homeobox protein
DNA binding 39 – 98 Homeobox


Literature citations

The leucine zipper of NRL interacts with the CRX homeodomain. A possible mechanism of transcriptional synergy in rhodopsin regulation.
Mitton K.P.; Swain P.K.; Chen S.; Xu S.; Zack D.J.; Swaroop A.;
J. Biol. Chem. 275:29794-29799(2000)
Cited for: INTERACTION WITH NRL; CHARACTERIZATION OF VARIANT CORD2 TRP-41; CHARACTERIZATION OF VARIANT LCA7 TRP-90;

Mutations in the cone-rod homeobox gene are associated with the cone-rod dystrophy photoreceptor degeneration.
Swain P.K.; Chen S.; Wang Q.-L.; Affatigato L.M.; Coats C.L.; Brady K.D.; Fishman G.A.; Jacobson S.G.; Swaroop A.; Stone E.; Sieving P.A.; Zack D.J.;
Neuron 19:1329-1336(1997)
Cited for: VARIANTS CORD2 TRP-41 AND MET-242; VARIANT RP GLN-41; VARIANT THR-158;

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.