UniProtKB/Swiss-Prot Q6VVX0: Variant p.Leu99Pro

Vitamin D 25-hydroxylase
Gene: CYP2R1
Chromosomal location: 11p15.2
Variant information

Variant position:  99
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Type of variant:  Disease [Disclaimer]
The variants are classified into three categories: Disease, Polymorphism and Unclassified.
  • Disease: Variants implicated in disease according to literature reports.
  • Polymorphism: Variants not reported to be implicated in disease.
  • Unclassified: Variants with uncertain implication in disease according to literature reports. Evidence against or in favor of a pathogenic role is limited and/or conflicting.

Residue change:  From Leucine (L) to Proline (P) at position 99 (L99P, p.Leu99Pro).
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

Involvement in disease:  Rickets vitamin D-dependent 1B (VDDR1B) [MIM:600081]: A disorder caused by a selective deficiency of the active form of vitamin D (1,25-dihydroxyvitamin D3) and resulting in defective bone mineralization and clinical features of rickets. The patients sera have low calcium concentrations, low phosphate concentrations, elevated alkaline phosphatase activity and low levels of 25-hydroxyvitamin D. {ECO:0000269|PubMed:15128933, ECO:0000269|PubMed:25942481}. Note=The disease is caused by mutations affecting the gene represented in this entry.
The name and a short description of the disease associated with the variant. For more information about the disease, the user can refer to OMIM, following the link provided after the disease acronym.

Variant description:  In VDDR1B; complete loss of activity.
Any additional useful information about the variant.

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



Sequence information

Variant position:  99
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:  501
The length of the canonical sequence.

Location on the sequence:   LDLGGISTVVLNGYDVVKEC  L VHQSEIFADRPCLPLFMKMT
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                         LDLGGISTVVLNGYDVVKECLVHQSEIFADRPCLPLFMKMT

Mouse                         LDLGGISTVVLNGYDVVKECLVHQSEIFADRPCLPLFMKMT

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 1 – 501 Vitamin D 25-hydroxylase
Helix 92 – 99


Literature citations

Genetic evidence that the human CYP2R1 enzyme is a key vitamin D 25-hydroxylase.
Cheng J.B.; Levine M.A.; Bell N.H.; Mangelsdorf D.J.; Russell D.W.;
Proc. Natl. Acad. Sci. U.S.A. 101:7711-7715(2004)
Cited for: VARIANT VDDR1B PRO-99;

CYP2R1 mutations impair generation of 25-hydroxyvitamin D and cause an atypical form of vitamin D deficiency.
Thacher T.D.; Fischer P.R.; Singh R.J.; Roizen J.; Levine M.A.;
J. Clin. Endocrinol. Metab. 100:E1005-1013(2015)
Cited for: VARIANT VDDR1B PRO-99; VARIANT ASN-242; CHARACTERIZATION OF VARIANT VDDR1B PRO-99; CHARACTERIZATION OF VARIANT ASN-242;

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.