UniProtKB/Swiss-Prot P05106: Variant p.Arg169Gln

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

169 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 Glutamine (Q) at position 169 (R169Q, p.Arg169Gln). 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 (Q) 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:

Position 59 is associated with platelet-specific alloantigen HPA-1 (ZW or PL(A)). HPA-1A/ZW(A)/PL(A1) has Leu-59 and HPA-1B/ZW(B)/PL(A2) has Pro-59. HPA-1A is involved in fetal-maternal alloimmune thromobocytopenia (FMAIT) as well as in neonatal alloimmune thrombocytopenia (NAIT).Position 169 is associated with platelet-specific alloantigen HPA-4 (PEN or YUK). HPA-4A/PEN(A)/YUK(A) has Arg-169 and HPA-4B/PEN(B)/YUK(B) has Gln-169. HPA-4B is involved in neonatal alloimmune thrombocytopenia (NAIT or NATP). - Position 433 is associated with platelet-specific alloantigen MO. MO(-) has Pro-433 and MO(+) has Ala-433. MO(+) is involved in NAIT. - Position 515 is associated with platelet-specific alloantigen CA/TU. CA(-)/TU(-) has Arg-515 and CA(+)/TU(+) has Gln-515. CA(+) is involved in NAIT. - Position 662 is associated with platelet-specific alloantigen SR(A). SR(A)(-) has Arg-662 and SR(A)(+) has Cys-662. - Additional information on the polymorphism described.
Variant description:

In alloantigen HPA-4B. Any additional useful information about the variant.
Other resources:

Links to websites of interest for the variant.

Variant rs5917 [ dbSNP | Ensembl ]

Sequence information Variant position:

169 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:

SMKDDLWSIQNLGTKLATQM R KLTSNLRIGFGAFVDKPVSP 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                         SMKDDLWSIQNLGTKLATQMRKLTSNLRIGFGAFVDKPVSP

Mouse                         SMKDDLSSIQTLGTKLASQMRKLTSNLRIGFGAFVDKPVSP

Rat                           SMKDDLSSIQTLGTKLASQMRKLTSNLRIGFGAFVDKPVSP

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
Domain	135 – 377	VWFA
Binding site	149 – 149	in ADMIDAS binding site
Binding site	149 – 149	in MIDAS binding site
Binding site	152 – 152	in ADMIDAS binding site
Binding site	153 – 153	in ADMIDAS binding site
Binding site	184 – 184	in LIMBS binding site
Disulfide bond	39 – 461
Turn	169 – 171

Literature citations
An amino acid polymorphism within the RGD binding domain of platelet membrane glycoprotein IIIa is responsible for the formation of the Pena/Penb alloantigen system.
Wang R.; Furihata K.; McFarland J.G.; Friedman K.; Aster R.H.; Newman P.J.;
J. Clin. Invest. 90:2038-2043(1992)
Cited for: VARIANT HPA-4B GLN-169; DESCRIPTION OF ALLOANTIGEN SYSTEM PEN; Characterization of single-nucleotide polymorphisms in coding regions of human genes.
Cargill M.; Altshuler D.; Ireland J.; Sklar P.; Ardlie K.; Patil N.; Shaw N.; Lane C.R.; Lim E.P.; Kalyanaraman N.; Nemesh J.; Ziaugra L.; Friedland L.; Rolfe A.; Warrington J.; Lipshutz R.; Daley G.Q.; Lander E.S.;
Nat. Genet. 22:231-238(1999)
Cited for: VARIANTS PRO-59; GLN-169 AND ILE-453;

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.