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UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q14749: Variant p.Leu50Pro

Glycine N-methyltransferase
Gene: GNMT
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Variant information Variant position: help 50 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 Leucine (L) to Proline (P) at position 50 (L50P, p.Leu50Pro). 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 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: 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 GNMT deficiency; 10% wild-type glycine N-methyltransferase activity. Any additional useful information about the variant.
Other resources: help Links to websites of interest for the variant.


Sequence information Variant position: help 50 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length: help 295 The length of the canonical sequence.
Location on the sequence: help VWQLYIGDTRSRTAEYKAWL L GLLRQHGCQRVLDVACGTGV 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                         VWQLYIGDTRSRTAEYKAWLLGLLRQHGCQRVLDVACGTGV

Mouse                         VWQLYIGDTRSRTAEYKAWLLGLLRQHGCHRVLDVACGTGV

Rat                           VWQLYIGDTRSRTAEYKAWLLGLLRQHGCHRVLDVACGTGV

Pig                           VWQLYIGDTRSRTAEYKAWLLGLLRQHGCQRVLDVACGTGV

Rabbit                        VWQLYIGDTRSRTSEYKTWLLGLLRQHGCRRVLDVACGTGV
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 2 – 295 Glycine N-methyltransferase
Binding site 31 – 31
Binding site 34 – 34
Binding site 41 – 41
Binding site 65 – 65
Modified residue 34 – 34 Phosphotyrosine
Modified residue 46 – 46 N6-succinyllysine
Helix 43 – 55



Literature citations
Mutations in human glycine N-methyltransferase give insights into its role in methionine metabolism.
Luka Z.; Cerone R.; Phillips J.A. III; Mudd S.H.; Wagner C.;
Hum. Genet. 110:68-74(2002)
Cited for: VARIANTS GNMT DEFICIENCY PRO-50 AND ASN-177; Effect of naturally occurring mutations in human glycine N-methyltransferase on activity and conformation.
Luka Z.; Wagner C.;
Biochem. Biophys. Res. Commun. 312:1067-1072(2003)
Cited for: CHARACTERIZATION OF VARIANTS GNMT DEFICIENCY PRO-50; SER-141 AND ASN-177; FUNCTION; CATALYTIC ACTIVITY; BIOPHYSICOCHEMICAL PROPERTIES;
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.