Genotype-phenotype association and variant characterization in Diamond-Blackfan anemia caused by pathogenic variants in RPL35A

Abstract

Diamond Blackfan anemia (DBA) is predominantly an autosomal dominant inherited red cell aplasia primarily caused by pathogenic germline variants in ribosomal protein genes. DBA due to pathogenic RPL35A variants has been associated with large 3q29 deletions and phenotypes not common in DBA. We conducted a multi-institutional genotype-phenotype study of 45 patients with DBA associated with pathogenic RPL35A germline variants and curated the variant data on 21 additional cases from the literature. Genotype-phenotype analyses were conducted comparing patients with large deletions versus all other pathogenic variants in RPL35A. Twenty-two of the 45 cases had large deletions in RPL35A. After adjusting for multiple tests, a statistically significant association was observed between patients with a large deletion and steroid-resistant anemia, neutropenia, craniofacial abnormalities, chronic gastrointestinal problems, and intellectual disabilities (p<0.01) compared with all other pathogenic variants. Non-large deletion pathogenic variants were spread across RPL35A with no apparent hot spot and 56% of the individual family variants were observed more than once. In this, the largest known study of DBA patients with pathogenic RPL35A variants, we determined that patients with large deletions have a more severe phenotype that is clinically different from those with non-large deletion variants. Genes of interest also deleted in the 3q29 region that could be associated with some of these phenotypic features include LMLN and IQCG. Management of DBA due to large RPL35A deletions may be challenging due to complex problems and require comprehensive assessments by multiple specialists including immunologic, gastrointestinal, and developmental evaluations to provide optimal multidisciplinary care.

Figures

Figure 1.

Study population and types of RPL35A variants in patients with Diamond-Blackfan anemia (DBA). NCI: National Cancer Institute Inherited Bone Marrow Failure Study; DBAR: DBA registry; HGMD: Human Gene Mutation Database; Alabama Children’s: Arkansas Children’s Hospital; Boston Children’s: Boston Children’s Hospital; UTR: untranslated regions; ClinVar: ClinVar public data archive.

Figure 2.

Distribution of RPL35A pathogenic variants reported in patients with Diamond-Blackfan anemia (DBA). All pathogenic single nucleotide and small indel variants are represented once per family. cDNA position based on transcript NM_000996.3. Numbers and letters indicate amino acids. Dotted lines indicate exons. Gray circles: literature, HGMD, and ClinVar cases. Black circles: collaborator cases. Cluster, defined as >5 unrelated cases by family in one area, is located between codon 28 to 33 (*). The numbers within the circles indicate the number of unique families with that specific pathogenic variant.

Figure 3.

Cases of RPL35A large deletions ordered by size in megabases (mB). Each horizontal bar represents the starting and stopping genomic co-ordinates of a RPL35A large deletion case. For literature cases without a case identification (ID) in article, the PubMed ID (PMID) was used as case ID (Online Supplementary Table S3). Thin black vertical lines indicate genomic starting and stopping co-ordinates of 3q29 deletion syndrome; thick black vertical line is the estimated location of RPL35A. See Online Supplementary Table S5 for exact genes deleted per case.