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UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q9NZR4: Variant p.Ala256Ser

Visual system homeobox 1
Gene: VSX1
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Variant information Variant position: help 256 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Type of variant: help 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: help From Alanine (A) to Serine (S) at position 256 (A256S, p.Ala256Ser). 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: help Change from small size and hydrophobic (A) to small size and polar (S) The physico-chemical property of the reference and variant residues and the change implicated.
BLOSUM score: help 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: help In CAASDS. Any additional useful information about the variant.
Other resources: help Links to websites of interest for the variant.


Sequence information Variant position: help 256 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length: help 365 The length of the canonical sequence.
Location on the sequence: help GLYGAMVRHCIPLPDSVLNS A EGGLLGSCAPWLLGMHKKSM 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: help The multiple alignment of the region surrounding the variant against various orthologous sequences. 
Human                         GLYGAMVRHCIPLPDSVLNSAEGGLLGSCAPWLL----GMHKKSM

Mouse                         GLYGAMVRHCIPLPDSVLNSADS-LQGSCAPWLL----GMH

Bovine                        GLYGAMVRHCIPLPDSVLGSGEGGLLGSCAPWLL----GMH

Chicken                       GLYGAMVRHSIPLPESIINSAKSGLVGSCAPWLL----GMH

Xenopus laevis                GLYGAMVRHSIPLPESIINSAKNGLVGSCAPWLL----GMH

Zebrafish                     GLYGAMVRHSIPLPESIINSAKSGMMGSCAPWLLGEPAGMH
Sequence annotation in neighborhood: help 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 219 – 365 Missing. In isoform 6.
Alternative sequence 237 – 365 Missing. In isoform 7.
Alternative sequence 240 – 365 Missing. In isoform 2 and isoform 3.



Literature citations
VSX1 (RINX) mutation with craniofacial anomalies, empty sella, corneal endothelial changes, and abnormal retinal and auditory bipolar cells.
Mintz-Hittner H.A.; Semina E.V.; Frishman L.J.; Prager T.C.; Murray J.C.;
Ophthalmology 111:828-836(2004)
Cited for: VARIANT CAASDS SER-256; VARIANT SER-131;
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.