UniProtKB/SwissProt variant VAR

Variant information

Variant position:

242

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 Arginine (R) to Cysteine (C) at position 242 (R242C, p.Arg242Cys).

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:

Change from large size and basic (R) to medium size and polar (C)

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:

Smith-Lemli-Opitz syndrome (SLOS) [MIM:270400]: An autosomal recessive frequent inborn disorder of sterol metabolism with characteristic congenital malformations and mental retardation. Children with SLOS have elevated serum 7-dehydrocholesterol (7-DHC) levels and low serum cholesterol levels. SLOS occurs in relatively high frequency: approximately 1 in 20,000 to 30,000 births in populations of northern and central European background. Historically, a clinical distinction often was made between classic ('type I') SLOS and the more severely affected ('type II') patients. There is, in reality, a clinical and biochemical continuum from mild to severe SLOS. {ECO:0000269|PubMed:10677299, ECO:0000269|PubMed:10995508, ECO:0000269|PubMed:11175299, ECO:0000269|PubMed:11427181, ECO:0000269|PubMed:12949967, ECO:0000269|PubMed:15954111, ECO:0000269|PubMed:9653161, ECO:0000269|PubMed:9683613}. 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 SLOS.

Any additional useful information about the variant.

Other resources:

Links to websites of interest for the variant.

Variant rs80338856 [ dbSNP | Ensembl ]

Sequence information

Variant position:

242

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

Protein sequence length:

475

The length of the canonical sequence.

Location on the sequence:

GIEFNPRIGKWFDFKLFFNG R PGIVAWTLINLSFAAKQREL

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                         GIEFNPRIGKWFDFKLFFNGRPGIVAWTLINLSFAAKQREL

Mouse                         GIEFNPRIGKWFDFKLFFNGRPGIVAWTLINLSFAAKQQEL

Rat                           GIEFNPRIGKWFDFKLFFNGRPGIVAWTLINLSFAAKQQEL

Bovine                        GVEFNPRIGKWFDFKLFFNGRPGIVAWTLINLSFAAKQQEL

Xenopus laevis                GIEFNPRIGKWFDFKLFFNGRPGIVAWTLINLSYAAKQQEL

Xenopus tropicalis            GIEFNPRIGKWFDFKLFFNGRPGIVAWTLINLSYAAKQQEL

Zebrafish                     GIEFNPRIGKWFDFKLFFNGRPGIVAWTLINLSYAAKQQEL

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.

Type	Positions	Description
Chain	1 – 475	7-dehydrocholesterol reductase

Literature citations

Mutational spectrum in the Delta7-sterol reductase gene and genotype-phenotype correlation in 84 patients with Smith-Lemli-Opitz syndrome.
Witsch-Baumgartner M.; Fitzky B.U.; Ogorelkova M.; Kraft H.G.; Moebius F.F.; Glossmann H.; Seedorf U.; Gillessen-Kaesbach G.; Hoffmann G.F.; Clayton P.; Kelley R.I.; Utermann G.;
Am. J. Hum. Genet. 66:402-412(2000)
Cited for: VARIANTS SLOS SER-51; MET-93; PRO-99; HIS-107; PRO-109; ASP-147; MET-154; PRO-157; LEU-169; CYS-182; CYS-242; VAL-247; MET-281; ILE-289; GLY-311; TYR-311; HIS-324; LEU-326; GLN-352; TRP-352; ALA-353; CYS-362; TYR-380; ARG-380; SER-380; LEU-397; CYS-404; SER-404; HIS-408; SER-410; ARG-410; CYS-443; GLN-446; GLN-448; LYS-448 AND LEU-450;

Identification of nine novel DHCR7 missense mutations in patients with Smith-Lemli-Opitz syndrome (SLOS).
Waye J.S.; Krakowiak P.A.; Wassif C.A.; Sterner A.L.; Eng B.; Nakamura L.M.; Nowaczyk M.J.M.; Porter F.D.;
Hum. Mutat. 26:59-59(2005)
Cited for: VARIANTS SLOS PRO-68; CYS-113; VAL-138; LEU-145; SER-235; CYS-242; THR-297; ARG-344; CYS-404; TYR-405; HIS-408 AND PRO-426;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q9UBM7: Variant p.Arg242Cys