Characterization of a novel HLA-C allele, HLA-C*05:278N

This report describes the identification and characterization of a novel HLA-C allele, HLA-C*05:278N, discovered during routine HLA typing. The context is histocompatibility testing for transplantation, where accurate allele resolution is critical. The aim was to define the sequence variation relative to HLA-C*05:01:01:02 and assess its likely functional impact.

Relevant resources include the IPD-IMGT/HLA Database for sequence submission and nomenclature, and the WHO HLA Nomenclature guidelines for allele naming. Prior work on nanopore sequencing has demonstrated its utility for rapid, comprehensive HLA typing in time-sensitive donor scenarios.

HLA typing was performed on a renal transplant candidate with Next-Generation Sequencing using NGSgo (GenDX, Utrecht, NL) on an Illumina MiSeq (San Diego, CA) and with NanoTYPE (Omixon Biocomputing Ltd, Budapest, Hungary) based on nanopore sequencing. FastQ reads were analyzed using NGSengine software (v2.26.1) and NanoTYPER software (v1.0.0). The patient’s HLA genotype included: HLA-A*02:01, 03:01; B*07:02, 44:02; C*05:278N, 07:02; DRB1*01:01, 04:07; DRB4*01:03; DQA1*01:01, 03:03; DQB1*03:01, 05:01; DPA1*01:03; DPB1*03:01, 04:01. Sequence comparison to HLA-C*05:01:01:02 identified a single G>A mismatch at nucleotide position 1767 in exon 4, changing codon 244 from TGG (Trp) to TGA (stop). Serological typing using micro-lymphocyte cytotoxicity was not performed due to lack of HLA-C–specific reagents. The full exon 1–8 sequence was submitted to GenBank (OP297268) and to the IPD-IMGT/HLA Database (submission HWS10062728).

- Novel allele HLA-C*05:278N differs from HLA-C*05:01:01:02 by one nucleotide (G>A) at position 1767 in exon 4. - This substitution converts codon 244 from TGG (tryptophan) to TGA (stop), introducing a premature termination codon. - The allele is predicted to be null, with no cell surface expression. - The sequence was deposited in GenBank (OP297268) and IPD-IMGT/HLA (HWS10062728), and the allele designation HLA-C*05:278N was officially assigned by the WHO Nomenclature Committee in January 2023.

Identification of a premature stop codon at position 244 strongly suggests that HLA-C*05:278N is a null allele lacking surface expression, which has implications for antigen presentation and histocompatibility assessments in transplantation. The finding, confirmed across two sequencing platforms and two analysis pipelines, supports the robustness of the variant call. Official assignment of the allele name and database submission ensures traceability and availability to the community.

This study reports and characterizes HLA-C*05:278N, a novel null allele distinguished by a single G>A substitution in exon 4 that creates a premature stop at codon 244. The allele has been deposited in public databases and officially named by the WHO HLA Nomenclature Committee. Future work could include functional validation of the predicted null phenotype through expression assays and broader population screening to determine allele frequency.

Serological confirmation could not be performed due to lack of HLA-C typing reagents. The characterization is based on a single individual, and functional consequence (lack of surface expression) is inferred from sequence rather than experimentally demonstrated.