A new HLA‐C allele with an alternative splice site in exon 3: HLA‐C*03:23N

Abstract

We identified a probable new null HLA‐C allele, C*03:23N, which originated from C*03:04:01:02, but does not react with Cw3 antibodies. This allele was identified by sequence analysis, which indicated that a single G‐to‐A substitution at position 406 in exon 3 created a null allele under a new mechanism: the mutation changes the position of the intron 2‐exon 3 splice site to be further into exon 3, leading to a frameshift and a premature stop codon. Sequence analysis of cDNA confirmed the existence of the causative alternative acceptor splice site and the resultant deletion of 64 nucleotides in exon 3. Analysis of 220 blood or bone marrow donors in Japan with C*03:23N demonstrated that Japanese HLA‐C*03:23N is on the haplotype A*26:01∼C*03:23N∼B*40:02∼DRB1*09:01.

Nucleotide alterations in the HLA-C class I gene can cause aberrant splicing and marked changes in RNA levels in a polymorphic context-dependent manner

“…In 14% of cases, the HLA-C exon 2 was spliced to a noncanonical exon-3 start at position 783 (see Figure 3B ), consistent with the alternate 3’-splice site on HLA-C*03:23N described by Shimizu et al. ( 32 ). This noncanonical start at position 783 appears to be generated by the A variation at position 781 inside the canonical exon 3, corresponding to -2 (minus 2) position of the alternate 3’ site.…”

“…The HLA-C*03:23N allele was described by Shimizu et al. as a null allele, originally based on low levels of cell-surface expression of the product ( 32 ). We searched for and identified three samples with HLA-C*03: 23 N in the sample-set that we originally collected for our previous HLA-expression analyses ( 15 ).…”

“…The HLA-C*03:23N was identified as a null allele by Shimizu et al. ( 32 ). They suggested that the G781A polymorphism within exon 3 on C*03:23N generates an efficient 3’ splice site within exon 3.…”

“…The purpose and mechanisms of alternative splicing of HLA class I genes for peptide presentation and regulation of T cell responses are still poorly understood. However, many null or low expression alleles of HLA class I genes have been reported including the HLA-C null allele, C*03:23N ( 32 ), which is the subject of the current work, and others ( 33 – 35 ). Although polymorphisms that influence RNA structure and abundance by modulating RNA splicing are anticipated to be widespread, they remain under-studied, with the exception of those leading to null or low-expression alleles.…”

Nomenclature for factors of the HLA system, update January, February and March 2020

“…The sequences for B*45:26 , B*78:01:01:01 , DQA1*03:01:01:02 and DQB1*02:02:06:01 have now been shown to be in error, therefore the allele names have been abandoned. The allele C*03:23 has be identified to have an alternative splice site 3 . To reflect this, the N suffix has been added to become C*03:23 N.…”