UniProtKB/SwissProt variant VAR

Variant information

Variant position:

42

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

Type of variant:

LB/B

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:

From Glycine (G) to Aspartate (D) at position 42 (G42D, p.Gly42Asp).

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 glycine (G) to medium size and acidic (D)

The physico-chemical property of the reference and variant residues and the change implicated.

BLOSUM score:

-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

Polymorphism:

DARC is responsible for the Duffy blood group system (FY) [MIM:110700]. The molecular basis of the Fy(A)=Fy1/Fy(B)=Fy2 blood group antigens is a single variation in position 42; Gly-42 corresponds to Fy(A) and Asp-42 to Fy(B). Individuals that do not produce the Duffy antigen (FY(A-B-)) are more resistant to infection by the malarial parasite Plasmodium vivax. This allele is found predominantly in population of African origin [MIM:611162].Genetic variations in DARC define the white blood cell count quantitative trait locus 1 (WBCQ1) [MIM:611862]. Peripheral white blood cell count (WBC) is a common clinical measurement, used to determine evidence of acute inflammation or infection. Peripheral WBC is the sum of several cell types including neutrophils and lymphocytes, which are the most common types of WBC, as well as less common cell types such as eosinophils, basophils, and monocytes. Elevated WBC has been associated with risk of coronary heart disease, cancer, and all-cause mortality. White blood cell levels have widespread clinical applications including assessment of patients undergoing chemotherapy and evaluation of infection. -

Additional information on the polymorphism described.

Variant description:

Antigen Fy(b).

Any additional useful information about the variant.

Other resources:

Links to websites of interest for the variant.

Variant rs12075 [ dbSNP | Ensembl ]

Sequence information

Variant position:

42

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

Protein sequence length:

336

The length of the canonical sequence.

Location on the sequence:

FEDVWNSSYGVNDSFPDGDY G ANLEAAAPCHSCNLLDDSAL

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                         FEDVWNSSYGVNDSFPDGDYGANLEAAAPCHSCNLLDDSAL

Gorilla                       FEDAWNSSYDVNYSFPDVDYDANLEAAAPCHSCNLLDDSAL

Rhesus macaque                S-DLWNFSYDGNDSFPDVDYDANLEAAAPCHSCNLLDDSAL

Chimpanzee                    FEDVWNSSYGVNDSFPDGDYDANLEAAAPCHSCNLLDDSAL

Mouse                         F-DSWNYSFEDNYSY-ELSSDYSLTPAAPCYSCNLLDRSSL

Bovine                        IKEDFLIDFPEDY-YPDYN-ETDVEAAAPCHSCSLLNYSSL

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 – 336	Atypical chemokine receptor 1
Topological domain	1 – 63	Extracellular
Glycosylation	33 – 33	N-linked (GlcNAc...) asparagine

Literature citations

Cloning of glycoprotein D cDNA, which encodes the major subunit of the Duffy blood group system and the receptor for the Plasmodium vivax malaria parasite.
Chaudhuri A.; Polyakova J.; Zbrzezna V.; Williams K.; Gulati S.; Pogo A.;
Proc. Natl. Acad. Sci. U.S.A. 90:10793-10797(1993)
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1); PARTIAL PROTEIN SEQUENCE; VARIANT ASP-42;

Disruption of a GATA motif in the Duffy gene promoter abolishes erythroid gene expression in Duffy-negative individuals.
Tournamille C.; Colin Y.; Cartron J.-P.; Le van Kim C.;
Nat. Genet. 10:224-228(1995)
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]; VARIANT ASP-42;

Arg89Cys substitution results in very low membrane expression of the Duffy antigen/receptor for chemokines in Fy(x) individuals.
Tournamille C.; Le Van Kim C.; Gane P.; Le Pennec P.Y.; Roubinet F.; Babinet J.; Cartron J.-P.; Colin Y.;
Blood 92:2147-2156(1998)
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (ISOFORM 2); VARIANTS ASP-42; CYS-89 AND THR-100;

The Fy(x) phenotype is associated with a missense mutation in the Fy(b) allele predicting Arg89Cys in the Duffy glycoprotein.
Olsson M.L.; Smythe J.S.; Hansson C.; Poole J.; Mallinson G.; Jones J.; Avent N.D.; Daniels G.;
Br. J. Haematol. 103:1184-1191(1998)
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1); VARIANTS ASP-42; CYS-89 AND THR-100;

Molecular basis and PCR-DNA typing of the Fya/fyb blood group polymorphism.
Tournamille C.; Le van Kim C.; Gane P.; Cartron J.-P.; Colin Y.;
Hum. Genet. 95:407-410(1995)
Cited for: VARIANT ASP-42;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q16570: Variant p.Gly42Asp