UniProtKB/Swiss-Prot P05106: Variant p.Arg662Cys

Integrin beta-3
Gene: ITGB3
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Variant information Variant position:

662 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 Arginine (R) to Cysteine (C) at position 662 (R662C, p.Arg662Cys). 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
Polymorphism:

Genetic variants in ITGB3 define different platelet-specific alloantigen systems that are involved in fetomaternal alloimmune thromobocytopenia. Alloantigen system Pl(A), also known as Zw or HPA-1, is characterized by variant p.Pro59Leu (alloantigen Pl(A1) or HPA-1A) and by variant p.Leu59Pro (alloantigen Pl(A2) or HPA-1B) (PubMed:2565345). Alloantigen system Pen, also known as Yuk or HPA-4, is characterized by variant p.Gln169Arg (alloantigen Pen(A)) and variant p.Arg169Gln (alloantigen Pen(B)) (PubMed:3798869, PubMed:1430225). Alloantigen system Mo is characterized by variant p.Pro433Ala (alloantigen Mo(+)) and variant p.Ala433Pro (alloantigen Mo(-)) (PubMed:8093349). Alloantigen system CA/TU is characterized by variant p.Gln515Arg (alloantigen CA(-)/TU(-)) and variant p.Arg515Gln (alloantigen CA(+)/TU(+)) (PubMed:7694683). Alloantigen system Sra is characterized by variant p.Cys662Arg (alloantigen Sra(-)) and variant p.Arg662Cys (alloantigen Sra(+)) (PubMed:8132570). Alloantigen system Sec(a) is characterized by variant p.Lys606Asn (alloantigen Sec(a+)) and variant p.Asn606Lys (alloantigen Sec(a-)) (PubMed:22116617). Additional platelet-specific alloantigens involved in fetomaternal alloimmune thromobocytopenia are known (PubMed:12036875, PubMed:19821948, PubMed:25494608, PubMed:28518345, PubMed:31859394). Additional information on the polymorphism described.
Variant description:

Found in alloantigen Sra(+). Any additional useful information about the variant.
Other resources:

Links to websites of interest for the variant.

Variant rs151219882 [ dbSNP | Ensembl ]

Sequence information Variant position:

662 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length:

788 The length of the canonical sequence.
Location on the sequence:

ECKKFDRGALHDENTCNRYC R DEIESVKELKDTGKDAVNCT 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                         ECKKFDRGALHDENTCNRYCRDEIESVKELKDTGKDAVNCT

Mouse                         ECKKFNRGTLHEENTCSRYCRDDIEQVKELTDTGKNAVNCT

Rat                           ECKKFNRGKLHEENNCNRFCRDDIELVKELTDTGKNAVNCT

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	27 – 788	Integrin beta-3
Topological domain	27 – 718	Extracellular
Glycosylation	680 – 680	N-linked (GlcNAc...) asparagine
Disulfide bond	634 – 681
Mutagenesis	659 – 659	R -> A. Slight increase in ligand-binding activity; when associated with 698-D--K-702 del.

Literature citations
A point mutation leads to an unpaired cysteine residue and a molecular weight polymorphism of a functional platelet beta 3 integrin subunit. The Sra alloantigen system of GPIIIa.
Santoso S.; Kalb R.; Kroll H.; Walka M.; Kiefel V.; Mueller-Eckhardt C.; Newman P.J.;
J. Biol. Chem. 269:8439-8444(1994)
Cited for: VARIANT CYS-662; POLYMORPHISM; DESCRIPTION OF ALLOANTIGEN SYSTEM SRA;

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.