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UniProtKB/Swiss-Prot P22061: Variant p.Val120Ile

Protein-L-isoaspartate(D-aspartate) O-methyltransferase
Gene: PCMT1
Variant information

Variant position:  120
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Type of variant:  LB/B
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 Isoleucine (I) at position 120 (V120I, p.Val120Ile).
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:  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

Polymorphism:  The allele frequencies for the polymorphism at codon 120 differ between ethnic groups; in the Caucasian population Ile-120 is present at a frequency of 0.45, while it is found at a frequency of 0.88 and 0.81 in the Asian and the African populations respectively. Val-120 is found at a frequency of 0.55 in the Caucasians, 0.12 and 0.19 in the Asian and African populations respectively. The Ile-120 variant has higher specific activity and thermostability than the Val-120 variant. The Val-120 variant has a higher affinity for protein substrates.
Additional information on the polymorphism described.

Other resources:  
Links to websites of interest for the variant.



Sequence information

Variant position:  120
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:  227
The length of the canonical sequence.

Location on the sequence:   VGCTGKVIGIDHIKELVDDS  V NNVRKDDPTLLSSGRVQLVV
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: 
The multiple alignment of the region surrounding the variant against various orthologous sequences.

Human                         VGCTG-----KVIGIDHIKELVDDSVNNVRKD---DPTLLS---SGRVQLVV

Mouse                         VGNSG-----KVIGIDHIKELVDDSITNVKKD---DPMLLS

Rat                           VGHSG-----KVIGIDHIKELVDDSITNVKKD---DPMLLS

Pig                           VGPSG-----KVIGIDHIKELVDDSINNVRKD---DPMLLS

Bovine                        VGPSG-----KVIGIDHIKELVDDSINNVRKD---DPMLLS

Chicken                       VGPKG-----QVVGIDHIKELVDDSINNVKKD---DPTLLS

Zebrafish                     VGPTG-----KVIGIDHIKELVEDSIANVKKD---DPSLIT

Caenorhabditis elegans        VGRNG-----TVVGIEHMPQLVELSEKNIRKH---HSEQLE

Drosophila                    IKAKGVDADTRIVGIEHQAELVRRSKANLNTD---DRSMLD

Slime mold                    MGCTG-----RVIGVEHIPELIERSIESIKRL---DSTLLD

Fission yeast                 VAPNG-----TVKGIEHIPQLVETSKKNLLKDINHDEVLME

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.

TypePositionsDescription
Chain 2 – 227 Protein-L-isoaspartate(D-aspartate) O-methyltransferase
Helix 113 – 126


Literature citations

Alternative splicing of the human isoaspartyl protein carboxyl methyltransferase RNA leads to the generation of a C-terminal -RDEL sequence in isozyme II.
Maclaren D.C.; Kagan R.M.; Clarke S.;
Biochem. Biophys. Res. Commun. 185:277-283(1992)
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2); VARIANT ILE-120;

The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).
The MGC Project Team;
Genome Res. 14:2121-2127(2004)
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2); VARIANT ILE-120;

Submission
Lubec G.; Afjehi-Sadat L.; Chen W.-Q.; Sun Y.;
Cited for: PROTEIN SEQUENCE OF 5-18; 25-37; 82-98; 114-144 AND 179-221; VARIANT ILE-120; IDENTIFICATION BY MASS SPECTROMETRY;

Distinct C-terminal sequences of isozymes I and II of the human erythrocyte L-isoaspartyl/D-aspartyl protein methyltransferase.
Ingrosso D.; Kagan R.M.; Clarke S.;
Biochem. Biophys. Res. Commun. 175:351-358(1991)
Cited for: PARTIAL PROTEIN SEQUENCE (ISOFORM 2); VARIANT ILE-120;

Polymorphic forms of the protein L-isoaspartate (D-aspartate) O-methyltransferase involved in the repair of age-damaged proteins.
DeVry C.G.; Clarke S.;
J. Hum. Genet. 44:275-288(1999)
Cited for: VARIANT ILE-120;

Initial characterization of the human central proteome.
Burkard T.R.; Planyavsky M.; Kaupe I.; Breitwieser F.P.; Buerckstuemmer T.; Bennett K.L.; Superti-Furga G.; Colinge J.;
BMC Syst. Biol. 5:17-17(2011)
Cited for: VARIANT [LARGE SCALE ANALYSIS] ILE-120; IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS];

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.