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UniProtKB/Swiss-Prot O43175: Variant p.Val490Met

D-3-phosphoglycerate dehydrogenase
Gene: PHGDH
Variant information

Variant position:  490
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Type of variant:  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:  From Valine (V) to Methionine (M) at position 490 (V490M, p.Val490Met).
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:  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:  In PHGDHD; results in almost undetectable enzyme activity with 3-phosphohydroxypyruvate.
Any additional useful information about the variant.

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



Sequence information

Variant position:  490
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:  533
The length of the canonical sequence.

Location on the sequence:   TQTSDPAMLPTMIGLLAEAG  V RLLSYQTSLVSDGETWHVMG
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                         TQTSDPAMLPTMIGLLAEAGVRLLSYQTSLVSDGETWHVMG

Chimpanzee                    TQTSDPAMPPTMMGLLAEAGVRLLSYQTSLVSDGETWHVMG

Mouse                         AQPSDPGMLPTMIGLLAEAGVQLLSYQTSMVSDGEPWHVMG

Rat                           AQPSDPVMLPTMIGLLAEAGVQLLSYQTSKVSDGDTWHVMG

Pig                           AQPSNPTMLPTMIGLLAEARVQLLSYQTSVVSDGETWHVMA

Bovine                        AQASNPAMLPTMIGLLAEAGVQLLSYQSSVVSDGETWHVMS

Slime mold                    -----------------------IGYIIADVDSEAS---KE

Baker's yeast                 -----------------------IAYLMADISSVDQSDIKD

Fission yeast                 -----------------------IAYLVADISDCTPGSLEA

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 – 533 D-3-phosphoglycerate dehydrogenase


Literature citations

Molecular characterization of 3-phosphoglycerate dehydrogenase deficiency -- a neurometabolic disorder associated with reduced L-serine biosynthesis.
Klomp L.W.J.; de Koning T.J.; Malingre H.E.M.; van Beurden E.A.C.M.; Brink M.; Opdam F.L.; Duran M.; Jaeken J.; Pineda M.; van Maldergem L.; Poll-The B.T.; van den Berg I.E.T.; Berger R.;
Am. J. Hum. Genet. 67:1389-1399(2000)
Cited for: NUCLEOTIDE SEQUENCE [MRNA]; VARIANTS PHGDHD MET-425 AND MET-490;

V490M, a common mutation in 3-phosphoglycerate dehydrogenase deficiency, causes enzyme deficiency by decreasing the yield of mature enzyme.
Pind S.; Slominski E.; Mauthe J.; Pearlman K.; Swoboda K.J.; Wilkins J.A.; Sauder P.; Natowicz M.R.;
J. Biol. Chem. 277:7136-7143(2002)
Cited for: CATALYTIC ACTIVITY; VARIANT MET-490;

Novel mutations in 3-phosphoglycerate dehydrogenase (PHGDH) are distributed throughout the protein and result in altered enzyme kinetics.
Tabatabaie L.; de Koning T.J.; Geboers A.J.J.M.; van den Berg I.E.T.; Berger R.; Klomp L.W.J.;
Hum. Mutat. 30:749-756(2009)
Cited for: VARIANTS PHGDHD TRP-135; MET-261; THR-373 AND SER-377; CHARACTERIZATION OF VARIANTS PHGDHD TRP-135; MET-261; THR-373; SER-377; MET-425 AND MET-490; 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.