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UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot P50747: Variant p.Val550Met

Biotin--protein ligase
Gene: HLCS
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Variant information Variant position: help 550 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 Valine (V) to Methionine (M) at position 550 (V550M, p.Val550Met). 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 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 HLCS deficiency. Any additional useful information about the variant.
Other resources: help Links to websites of interest for the variant.


Sequence information Variant position: help 550 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length: help 726 The length of the canonical sequence.
Location on the sequence: help LRSQLGQRIPFVQHLMSVAV V EAVRSIPEYQDINLRVKWPN 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                         LRSQLGQR---IPFVQHLMSVAVVEAVRS-IPEYQDINLRVKWPN

Mouse                         LRSQLGQR---IPFVQHLMSLAVVEAVRS-IPGYEDINLRV

Baker's yeast                 LQSPVTNRNISVVFVQYLSMLAYCKAILSYAPGFSDIPVRI

Fission yeast                 AKNFSTTP---IALFQYLMALAVVRGIREYAPGYENIPAFI
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 – 726 Biotin--protein ligase
Domain 463 – 652 BPL/LPL catalytic



Literature citations
Structure of human holocarboxylase synthetase gene and mutation spectrum of holocarboxylase synthetase deficiency.
Yang X.; Aoki Y.; Li X.; Sakamoto O.; Hiratsuka M.; Kure S.; Taheri S.; Christensen E.; Inui K.; Kubota M.; Ohira M.; Ohki M.; Kudoh J.; Kawasaki K.; Shibuya K.; Shintani A.; Asakawa S.; Minoshima S.; Shimizu N.; Narisawa K.; Matsubara Y.; Suzuki Y.;
Hum. Genet. 109:526-534(2001)
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]; VARIANTS HLCS DEFICIENCY ASP-42; PRO-237; GLU-333; SER-360; CYS-456; SER-470; TRP-508; GLY-547; MET-550; SER-581; THR-610 DEL AND TYR-634; CHARACTERIZATION OF VARIANTS HLCS DEFICIENCY ASP-42; SER-360; CYS-456; SER-470; GLY-547 AND TYR-634; Clustering of mutations in the biotin-binding region of holocarboxylase synthetase in biotin-responsive multiple carboxylase deficiency.
Dupuis L.; Leon-Del-Rio A.; Leclerc D.; Campeau E.; Sweetman L.; Saudubray J.-M.; Herman G.; Gibson K.M.; Gravel R.A.;
Hum. Mol. Genet. 5:1011-1016(1996)
Cited for: VARIANTS HLCS DEFICIENCY ARG-216; ASP-363; TRP-508; GLU-518; MET-550 AND ASN-571; Characterization of mutant holocarboxylase synthetase (HCS): a Km for biotin was not elevated in a patient with HCS deficiency.
Aoki Y.; Suzuki Y.; Li X.; Sakamoto O.; Chikaoka H.; Takita S.; Narisawa K.;
Pediatr. Res. 42:849-854(1997)
Cited for: VARIANTS HLCS DEFICIENCY PRO-237 AND MET-550; A genomic approach to mutation analysis of holocarboxylase synthetase gene in three Chinese patients with late-onset holocarboxylase synthetase deficiency.
Tang N.L.S.; Hui J.; Yong C.K.K.; Wong L.T.K.; Applegarth D.A.; Vallance H.D.; Law L.K.; Fung S.L.M.; Mak T.W.L.; Sung Y.M.; Cheung K.L.; Fok T.F.;
Clin. Biochem. 36:145-149(2003)
Cited for: VARIANTS HLCS DEFICIENCY TRP-508; MET-550 AND ASN-634;
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.