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UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot P35520: Variant p.Leu539Ser

Cystathionine beta-synthase
Gene: CBS
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Variant information Variant position: help 539 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 Serine (S) at position 539 (L539S, p.Leu539Ser). 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 hydrophobic (L) to small size and polar (S) The physico-chemical property of the reference and variant residues and the change implicated.
BLOSUM score: help -2 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 CBSD; loss of cystathionine beta-synthase activity; impaired stimulation by AdoMet and AdoHcy; loss of homotetramer formation. Any additional useful information about the variant.
Other resources: help Links to websites of interest for the variant.


Sequence information Variant position: help 539 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length: help 551 The length of the canonical sequence.
Location on the sequence: help HSTGKSSQRQMVFGVVTAID L LNFVAAQERDQK 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                         H--------------STGKSSQRQMVFGVVTAIDLLNFVAAQERDQK

Mouse                         RDQAWSGVVGGPTDCSNGMSSKQQMVFGVVTAI

Rat                           RDQAWSGVVGGPTDRNNGVSSKQLMVFGVVTAI

Rabbit                        G--------------GDEQPSKRQTVFGVVTAM

Slime mold                    --------------------TENDEIISIVTKI

Baker's yeast                 ---------------TDGLKP-----IHIVTKM
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 1 – 551 Cystathionine beta-synthase
Helix 536 – 544



Literature citations
Cystathionine beta-synthase mutations: effect of mutation topology on folding and activity.
Kozich V.; Sokolova J.; Klatovska V.; Krijt J.; Janosik M.; Jelinek K.; Kraus J.P.;
Hum. Mutat. 31:809-819(2010)
Cited for: CHARACTERIZATION OF VARIANTS CBSD LEU-49; ARG-65; ARG-78; ASN-102; VAL-114; GLN-125; LYS-144; ARG-148; TYR-165; LYS-176; ALA-180; MET-191; LYS-228; ARG-262; LYS-266; THR-278; LYS-302; ARG-305; SER-307; CYS-369; LEU-422; THR-435; GLN-439; ASN-444; LEU-466 AND SER-539; FUNCTION; CATALYTIC ACTIVITY; PATHWAY; ACTIVITY REGULATION; SUBUNIT; Two novel mutations (K384E and L539S) in the C-terminal moiety of the cystathionine beta-synthase protein in two French pyridoxine-responsive homocystinuria patients.
Aral B.; Coude M.; London J.; Aupetit J.; Chasse J.-F.; Zabot M.-T.; Chadefaux-Vekemans B.; Kamoun P.;
Hum. Mutat. 9:81-82(1997)
Cited for: VARIANTS CBSD GLU-384 AND SER-539;
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.