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UniProtKB/Swiss-Prot O43819: Variant p.Ala259Val

Protein SCO2 homolog, mitochondrial
Gene: SCO2
Variant information

Variant position:  259
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 Alanine (A) to Valine (V) at position 259 (A259V, p.Ala259Val).
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

Involvement in disease:  Myopia 6 (MYP6) [MIM:608908]: A refractive error of the eye, in which parallel rays from a distant object come to focus in front of the retina, vision being better for near objects than for far. {ECO:0000269|PubMed:23643385, ECO:0000269|PubMed:25525168, ECO:0000269|PubMed:25959673}. 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 MYP6.
Any additional useful information about the variant.

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

Sequence information

Variant position:  259
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:  266
The length of the canonical sequence.

Location on the sequence:   DYYGRSRSAEQISDSVRRHM  A AFRSVLS
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                         DYYGRSRSAEQISDSVRRHMAAFRS--------------VLS-

Mouse                         DYYGRSRSAEQIVESIRRHIAAFHS---

Bovine                        DYYSRARSAEQITDSVRRHMAAFRS---

Zebrafish                     DYYNRMKNDTQIAESIRNHMKTFVR---

Baker's yeast                 DALGRNYDEQSGLEKIREQIQAYVPKEE

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.

Chain 42 – 266 Protein SCO2 homolog, mitochondrial
Topological domain 79 – 266 Mitochondrial intermembrane
Domain 85 – 259 Thioredoxin
Helix 247 – 261

Literature citations

Mutations in SCO2 are associated with autosomal-dominant high-grade myopia.
Tran-Viet K.N.; Powell C.; Barathi V.A.; Klemm T.; Maurer-Stroh S.; Limviphuvadh V.; Soler V.; Ho C.; Yanovitch T.; Schneider G.; Li Y.J.; Nading E.; Metlapally R.; Saw S.M.; Goh L.; Rozen S.; Young T.L.;
Am. J. Hum. Genet. 92:820-826(2013)
Cited for: VARIANTS MYP6 HIS-114; LYS-140 AND VAL-259;

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.