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UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot P23378: Variant p.Arg461Trp

Glycine dehydrogenase (decarboxylating), mitochondrial
Gene: GLDC
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Variant information Variant position: help 461 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 Arginine (R) to Tryptophan (W) at position 461 (R461W, p.Arg461Trp). 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 basic (R) to large size and aromatic (W) The physico-chemical property of the reference and variant residues and the change implicated.
BLOSUM score: help -3 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 NKH; decreased glycine catabolic process; changed localization to the mitochondria; also expressed diffusely throughout the cytosol; decreased abundance. Any additional useful information about the variant.
Other resources: help Links to websites of interest for the variant.


Sequence information Variant position: help 461 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length: help 1020 The length of the canonical sequence.
Location on the sequence: help QCGCSVKEVLGRAAQRQINF R LFEDGTLGISLDETVNEKDL 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                         QCGCSV-KEVLGRAAQRQINFRLF--EDGTLGISLDETVNEKDL

Mouse                         QCGCSV-KEVLGRAAQRQINFRLF--DDGTLGISLDETVTE

Chicken                       TCGCSV-KEVLDRAALRKINVRIY--SDGRLGVSLDETVNE

Slime mold                    ITGDKT-DMMIKELESRQINVRQY--CSKSISISLDETVTS

Baker's yeast                 KLGNGISSEQLLDKALKEFNINLFAVDTTTISLALDETTTK

Fission yeast                 EVESA--DKVLAKALDHGYNLRKV--DDSHVGLSLDETVCD
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 36 – 1020 Glycine dehydrogenase (decarboxylating), mitochondrial
Modified residue 447 – 447 N6-acetyllysine



Literature citations
Nonketotic Hyperglycinemia: functional assessment of missense variants in GLDC to understand phenotypes of the disease.
Bravo-Alonso I.; Navarrete R.; Arribas-Carreira L.; Perona A.; Abia D.; Couce M.L.; Garcia-Cazorla A.; Morais A.; Domingo R.; Ramos M.A.; Swanson M.A.; Van Hove J.L.; Ugarte M.; Perez B.; Perez-Cerda C.; Rodriguez-Pombo P.;
Hum. Mutat. 38:678-691(2017)
Cited for: FUNCTION; SUBCELLULAR LOCATION; CATALYTIC ACTIVITY; INVOLVEMENT IN NKH; VARIANTS NKH LYS-146; PRO-173; ALA-267; CYS-362; TRP-373; GLU-376; TRP-461; PRO-548; TYR-580; ARG-581; ASP-624; ASP-763; GLU-768; TRP-790; HIS-866; GLY-905; THR-933 AND ARG-994; CHARACTERIZATION OF VARIANTS NKH LYS-146; PRO-173; ALA-267; CYS-362; TRP-373; GLU-376; TRP-461; PRO-548; TYR-580; ARG-581; ASP-624; ASP-763; GLU-768; TRP-790; HIS-866; GLY-905; THR-933 AND ARG-994;
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.