UniProtKB/Swiss-Prot Q99714: Variant p.Val176Met

• Variant information
• Sequence information
• Literature citations
• All

Variant information

Variant position: 176 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Type of variant: LP/P [Disclaimer: Variants classification is intended for research purposes only, not for clinical and diagnostic use. The label disease variant is assigned according to literature reports on probable disease-association that can be based on theoretical reasons. This label must not be considered as a definitive proof for the pathogenic role of a variant.] 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 Valine (V) to Methionine (M) at position 176 (V176M, p.Val176Met). 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: Similar physico-chemical property. Both residues are medium size and hydrophobic. The physico-chemical property of the reference and variant residues and the change implicated.
BLOSUM score: 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: In HSD10MD; decreased dehydrogenase activity; strongly decreased tRNA methylation; strongly decreased mitochondrial tRNA 5'-end processing. Any additional useful information about the variant.

Sequence information

Variant position: 176 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length: 261 The length of the canonical sequence.
Location on the sequence: VAAFEGQVGQAAYSASKGGI V GMTLPIARDLAPIGIRVMTI 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.
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.

Type	Positions	Description
Chain	2 – 261	3-hydroxyacyl-CoA dehydrogenase type-2
Active site	168 – 168	Proton acceptor
Binding site	168 – 168
Binding site	172 – 172
Mutagenesis	172 – 172	K -> A. Abolishes dehydrogenase activity. Does not affect mitochondrial tRNA 5'-end processing. Does not affect tRNA methylation. Does not affect homotetramerization.
Helix	166 – 186

Literature citations

Novel patient missense mutations in the HSD17B10 gene affect dehydrogenase and mitochondrial tRNA modification functions of the encoded protein.
Oerum S.; Roovers M.; Leichsenring M.; Acquaviva-Bourdain C.; Beermann F.; Gemperle-Britschgi C.; Fouilhoux A.; Korwitz-Reichelt A.; Bailey H.J.; Droogmans L.; Oppermann U.; Sass J.O.; Yue W.W.;
Biochim. Biophys. Acta 1863:3294-3302(2017)
Cited for: VARIANTS HSD10MD LEU-12 AND MET-176; FUNCTION; CATALYTIC ACTIVITY; BIOPHYSICOCHEMICAL PROPERTIES; SUBUNIT; CHARACTERIZATION OF VARIANTS HSD10MD LEU-12 AND MET-176;