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UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot P31327: Variant p.Thr544Met

Carbamoyl-phosphate synthase [ammonia], mitochondrial
Gene: CPS1
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Variant information Variant position: help 544 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 Threonine (T) to Methionine (M) at position 544 (T544M, p.Thr544Met). 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 polar (T) to medium size and hydrophobic (M) 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 CPS1D; almost complete loss of enzyme activity; approximately 60-fold increase in the apparent Km for bicarbonate and approximately 4-fold respective decrease and increase in the apparent Vmax and Km for ammonia. Any additional useful information about the variant.
Other resources: help Links to websites of interest for the variant.


Sequence information Variant position: help 544 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length: help 1500 The length of the canonical sequence.
Location on the sequence: help GVLKEYGVKVLGTSVESIMA T EDRQLFSDKLNEINEKIAPS 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                         GVLKEYGVKVLGTSVESIMATEDRQLFSDKLNEINEKIAPS

Mouse                         GVLKEYGVKVLGTSVESIMATEDRQLFSDKLNEINEKIAPS

Rat                           GVLKEYGVKVLGTSVESIMATEDRQLFSDKLNEINEKIAPS
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 39 – 1500 Carbamoyl-phosphate synthase [ammonia], mitochondrial
Modified residue 527 – 527 N6-acetyllysine; alternate
Modified residue 527 – 527 N6-glutaryllysine; alternate
Modified residue 527 – 527 N6-succinyllysine; alternate
Modified residue 532 – 532 N6-acetyllysine; alternate
Modified residue 532 – 532 N6-glutaryllysine; alternate
Modified residue 537 – 537 Phosphoserine; alternate
Modified residue 540 – 540 Phosphoserine
Modified residue 553 – 553 N6-acetyllysine; alternate
Modified residue 553 – 553 N6-glutaryllysine; alternate
Modified residue 553 – 553 N6-succinyllysine; alternate
Modified residue 560 – 560 N6-acetyllysine; alternate
Modified residue 560 – 560 N6-succinyllysine; alternate
Glycosylation 537 – 537 O-linked (GlcNAc) serine; alternate
Helix 538 – 545



Literature citations
Prenatal diagnosis of carbamoyl phosphate synthetase I deficiency by identification of a missense mutation in CPS1.
Finckh U.; Kohlschuetter A.; Schaefer H.; Sperhake K.; Colombo J.-P.; Gal A.;
Hum. Mutat. 12:206-211(1998)
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1); VARIANT CPS1D MET-544; VARIANT ALA-344; Molecular defects in human carbamoyl phosphate synthetase I: mutational spectrum, diagnostic and protein structure considerations.
Haberle J.; Shchelochkov O.A.; Wang J.; Katsonis P.; Hall L.; Reiss S.; Eeds A.; Willis A.; Yadav M.; Summar S.; Lichtarge O.; Rubio V.; Wong L.J.; Summar M.;
Hum. Mutat. 32:579-589(2011)
Cited for: VARIANTS CPS1D VAL-43; ASP-58; PHE-65; GLY-71; SER-87; ASP-89; GLY-165; VAL-224; CYS-233; PRO-243; GLU-258; GLU-263; VAL-304; GLU-317; HIS-358; LEU-382; ARG-401; ARG-431; VAL-432; THR-438; GLU-450; PRO-498; GLU-531; GLY-531; MET-544; CYS-587; HIS-587; LEU-587; LEU-597; MET-622; ASP-628; ARG-632; PRO-638; TYR-648; VAL-654; LYS-674; SER-698; LYS-718; GLN-721; PRO-724; THR-726; VAL-767; HIS-780; ILE-792; SER-803; GLY-803; CYS-803; SER-805; TRP-814; ARG-816; HIS-850; GLU-911; LEU-913; HIS-914; GLY-914; THR-932; THR-949; CYS-959; CYS-962; GLU-978; VAL-982; HIS-984; THR-986; CYS-987; SER-992; SER-1016; LEU-1017; ILE-1022; GLY-1034; ARG-1045; ARG-1059; GLU-1065; CYS-1089; GLU-1155; VAL-1155; LEU-1203; GLN-1228; ASP-1255; GLN-1262; PRO-1262; HIS-1274; ARG-1327; GLU-1333; LEU-1371; MET-1391; VAL-1398; LEU-1439; TRP-1453 AND ARG-1462; Molecular characterization of carbamoyl-phosphate synthetase (CPS1) deficiency using human recombinant CPS1 as a key tool.
Diez-Fernandez C.; Martinez A.I.; Pekkala S.; Barcelona B.; Perez-Arellano I.; Guadalajara A.M.; Summar M.; Cervera J.; Rubio V.;
Hum. Mutat. 34:1149-1159(2013)
Cited for: VARIANTS CPS1D ASP-355; CYS-389; ARG-390; PRO-438; MET-544; THR-1378; SER-1381 AND ALA-1443; VARIANTS ALA-344 AND SER-1376; CHARACTERIZATION OF VARIANTS CPS1D ASP-355; CYS-389; ARG-390; PRO-438; MET-544; THR-1378; SER-1381 AND ALA-1443; CHARACTERIZATION OF VARIANTS ALA-344 AND SER-1376; SUBUNIT; PROTEOLYTIC CLEAVAGE; BIOPHYSICOCHEMICAL PROPERTIES; ACTIVITY REGULATION; CATALYTIC ACTIVITY;
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.