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UniProtKB/Swiss-Prot Q9HD40: Variant p.Ala239Thr

O-phosphoseryl-tRNA(Sec) selenium transferase
Gene: SEPSECS
Variant information

Variant position:  239
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 Threonine (T) at position 239 (A239T, p.Ala239Thr).
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 polar (T)
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:  Pontocerebellar hypoplasia 2D (PCH2D) [MIM:613811]: A disorder characterized by postnatal onset of progressive atrophy of the cerebrum and cerebellum, microcephaly, profound mental retardation, spasticity, and variable seizures. {ECO:0000269|PubMed:20920667, ECO:0000269|PubMed:26115735}. 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 PCH2D; abrogates enzyme activity.
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:  501
The length of the canonical sequence.

Location on the sequence:   CIHSTTSCFAPRVPDRLEEL  A VICANYDIPHIVNNAYGVQS
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                         CIHSTTSCFAPRVPDRLEELAVICANYDIPHIVNNAYGVQS

Mouse                         CLHSTTACFAPRVPDRLEELAVICANYDIPHVVNNAYGLQS

Xenopus tropicalis            CVHSTTSCFAPRVPDRVEELAVICKKYEIPHVVNNAYGVQS

Zebrafish                     CVHSTTSCFAPRVPDRLEELSVLCAKHDIPHIVNNAYGVQP

Caenorhabditis elegans        CVMTTTSCFAPRSPDNVEAISAICAAHDVPHLVNNAYGLQS

Slime mold                    CVFSTTSCFAPRVPDKIIEISEICKRYNIGHIINNAYGLQC

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 – 501 O-phosphoseryl-tRNA(Sec) selenium transferase
Alternative sequence 48 – 501 Missing. In isoform 2.
Helix 235 – 244


Literature citations

Mutations disrupting selenocysteine formation cause progressive cerebello-cerebral atrophy.
Agamy O.; Ben Zeev B.; Lev D.; Marcus B.; Fine D.; Su D.; Narkis G.; Ofir R.; Hoffmann C.; Leshinsky-Silver E.; Flusser H.; Sivan S.; Soll D.; Lerman-Sagie T.; Birk O.S.;
Am. J. Hum. Genet. 87:538-544(2010)
Cited for: VARIANTS PCH2D THR-239 AND CYS-334; CHARACTERIZATION OF VARIANTS PCH2D THR-239 AND CYS-334;

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.