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J Clin Lab Anal. 2018 May;32(4):e22330. doi: 10.1002/jcla.22330. Epub 2017 Sep 19.

The synonymous nucleotide substitution RHD 1056C>G alters mRNA splicing associated with serologically weak D phenotype.

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Department of Laboratory Medicine & Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.
Samsung Advanced Institute of Health Science and Technology, Sungkyunkwan University, Seoul, Korea.
Department of Laboratory Medicine, Chosun University College of Medicine, Gwangju, Korea.
Stem Cell & Regenerative Medicine Institute, Samsung Medical Center, Seoul, Korea.



D antigen is one of the most clinically significant blood group antigens. Variation of the RHD gene can cause weak D or partial D phenotypes. While most variations are missense substitutions with amino acid changes, those without are called "silent" or "synonymous" substitutions. Synonymous substitutions often have little effect on the protein, not altering the phenotype. However, effect on splicing can affect end-product protein. We report a new synonymous variation, RHD 1056C>G, that resulted in weak D phenotype, and predicted its effect with various in silico methods.


Serologic testing of the D antigen with full sequencing of the RHD gene was done. Human Splice Finder was used to predict the effect of this variation, and validation of this method was done with all known RHD variations reported in the literature.


RHD 1056C>G was predicted to cause the formation of an exonic splicing silencer (ESS) site. The creation of new ESS site potentially inhibits the splicing event, resulting alteration of splicing. This is similar to remodeling of splice acceptor or donor site, as this kind of deep exonic variation could affect the D antigen's quality or quantity. This is in concordance with serologic results, which showed only delayed weak agglutination to anti-D reagents.


The analytic methods we applied showed good correlation with the actual phenotype, along with concordant results when analyzing other known variants reported in the literature. We conclude that RHD 1056C>G results in serologic weak D phenotype.


RHD ; genotype; in silico; silent; splicing; synonymous

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