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UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot P54868: Variant p.Phe470Thr

Hydroxymethylglutaryl-CoA synthase, mitochondrial
Gene: HMGCS2
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Variant information Variant position: help 470 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 Phenylalanine (F) to Threonine (T) at position 470 (F470T, p.Phe470Thr). 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 large size and aromatic (F) to medium size and polar (T) The physico-chemical property of the reference and variant residues and the change implicated.
BLOSUM score: help -2 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 HMGCS2D; decreased protein abundance; abolished enzymatic activity; requires 2 nucleotide substitutions. Any additional useful information about the variant.


Sequence information Variant position: help 470 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length: help 508 The length of the canonical sequence.
Location on the sequence: help ASRKCVSPEEFTEIMNQREQ F YHKVNFSPPGDTNSLFPGTW 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                         ASRKCVSPEEFTEIMNQREQFYHKVNFSPPGDTNSLFPGTW

Mouse                         DSRRRMSPEEFTEIMNQREQFYHKVNFSPPGDTSNLFPGTW

Rat                           DSRRRMSPEEFTEIMNQREQFYHKVNFSPPGDTSNLFPGTW

Pig                           ASRKRVSPEEFTEIMNQREQYYHKVNFTPPGDPNSLFPGTW

Bovine                        ASRKRVSPEEFTEIMNQREQYYHKMNFSPPGDKNSLFPGTW
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 38 – 508 Hydroxymethylglutaryl-CoA synthase, mitochondrial
Modified residue 456 – 456 Phosphoserine
Modified residue 473 – 473 N6-acetyllysine; alternate
Modified residue 473 – 473 N6-succinyllysine; alternate
Modified residue 477 – 477 Phosphoserine
Helix 457 – 470



Literature citations
Mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency: urinary organic acid profiles and expanded spectrum of mutations.
Pitt J.J.; Peters H.; Boneh A.; Yaplito-Lee J.; Wieser S.; Hinderhofer K.; Johnson D.; Zschocke J.;
J. Inherit. Metab. Dis. 38:459-466(2015)
Cited for: VARIANTS HMGCS2D SER-168; ASP-169; ARG-185; VAL-232; SER-266; PRO-360; THR-470; CYS-503 AND GLN-505;
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.