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UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot P34897: Variant p.Pro499Ala

Serine hydroxymethyltransferase, mitochondrial
Gene: SHMT2
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Variant information Variant position: help 499 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 Proline (P) to Alanine (A) at position 499 (P499A, p.Pro499Ala). 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 medium size and hydrophobic (P) to small size and hydrophobic (A) 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 NEDCASB; no effect on protein abundance; decreased glycine hydroxymethyltransferase activity; associated with altered mitochondrial redox metabolism. Any additional useful information about the variant.
Other resources: help Links to websites of interest for the variant.


Sequence information Variant position: help 499 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length: help 504 The length of the canonical sequence.
Location on the sequence: help SQRLANLRQRVEQFARAFPM P GFDEH 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                         SQRLANLRQRVEQFARAFPMPGFDEH

Mouse                         SQRLANLRQQVEQFARGFPMPGFDER

Bovine                        SHQLADLRQRVEQFARAFPMPGFDDH

Rabbit                        SQHLADLRRRVQQFARAFPMPGFPEH

Baker's yeast                 SSEVAALSGEISKWVGQYPVPG--DI

Fission yeast                 FSEIAKLKKEVITWAGKFDFPV----
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 30 – 504 Serine hydroxymethyltransferase, mitochondrial



Literature citations
Impairment of the mitochondrial one-carbon metabolism enzyme SHMT2 causes a novel brain and heart developmental syndrome.
Garcia-Cazorla A.; Verdura E.; Julia-Palacios N.; Anderson E.N.; Goicoechea L.; Planas-Serra L.; Tsogtbaatar E.; Dsouza N.R.; Schlueter A.; Urreizti R.; Tarnowski J.M.; Gavrilova R.H.; Ruiz M.; Rodriguez-Palmero A.; Fourcade S.; Cogne B.; Besnard T.; Vincent M.; Bezieau S.; Folmes C.D.; Zimmermann M.T.; Klee E.W.; Pandey U.B.; Artuch R.; Cousin M.A.; Pujol A.;
Acta Neuropathol. 140:971-975(2020)
Cited for: INVOLVEMENT IN NEDCASB; VARIANTS NEDCASB SER-157; ARG-186; ASP-379; SER-423; PRO-435 AND ALA-499; CHARACTERIZATION OF VARIANT NEDCASB ALA-499; FUNCTION; CATALYTIC ACTIVITY; PATHWAY;
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.