Submission Details

LRRC56 and Primary Ciliary Dyskinesia 39, autosomal recessive

Primary Ciliary Dyskinesia (PCD) is a genetically heterogeneous group of disorders, usually beginning in early childhood, characterized by chronic cough, recurrent infections of the upper and lower respiratory tract, randomization of left/right body asymmetry, and subfertility (PMID: 32943623). A subset of PCD cases have complex congenital heart defects (PMID: 17515466). The PCD phenotype results from structural and/or functional abnormalities of motile cilia and flagella. Ciliary motility is powered by a set of axoneme-specific dynein motor complexes. The cytoplasmic assembly of these large multiprotein complexes is assisted by dynein axonemal assembly factors and their subsequent transport into cilia is facilitated by proteins involved in the intraflagellar transport system (IFT).

Mutations in genes encoding proteins involved in the assembly or transport of these complexes can result in the improper assembly of dynein chains or impaired transport of complexes into the axoneme, causing defects in outer and/or inner dynein arms (ODAs and/or IDAs) that can result in ciliary immotility or dysfunction (PMID: 31624012). ODAs are actively transported into cilia via the IFT system before attachment to microtubule doublets via the docking complex (PMIDs: 30133350, 33473120). LRRC56 (Leucine-Rich Repeat-Containing Protein 56) has been shown to be a transient cargo of IFT trains during flagellum construction (PMID: 38865178). It has been proposed that LRRC56 plays a role in the cytoplasmic maturation and intraflagellar transport of ODAs during flagellar assembly (PMID: 25558044). It has also been suggested that it may play a role in the assembly of the dynein docking complex, perhaps as a transport adaptor (PMID: 38865178), or in aiding dyneins to bind with the axonemal docking complex (PMID: 25558044).

The LRRC56 gene was first reported in relation to PCD in patients by Bonnefoy et al. in 2018 (PMID: 30388400). The specific disease entity, Primary Ciliary Dyskinesia 39 is an autosomal recessive disorder caused by homozygous or compound heterozygous mutation in the LRRC56 gene. Per criteria outlined by the ClinGen Lumping and Splitting Working Group, we found the molecular mechanism and autosomal recessive mode of inheritance to be consistent among unrelated patients, while the phenotypic variability among them appeared to represent a spectrum of disease rather than separate disease entities. Therefore, cases caused by inherited LRRC56 variants have been lumped into a single disease entity, Primary Ciliary Dyskinesia 39 (MONDO:0032637, OMIM # 618254).

Genetic evidence from six probands, in four publications have been evaluated in this curation (PMIDs: 30388400, 36176820, 37892347, 39009665). Two of these probands were fetal patients that carried biallelic LRRC56 mutations (1 frameshift, 1 nonsense, and 1 missense), had laterality and in one case cardiac defects, but could not be assessed for respiratory symptoms for a PCD diagnosis. These patients’ pregnancies were terminated due to the risk of lethal defects. Four unique variants were scored from the remaining four probands (2 splice site, 1 missense, and 1 nonsense variant). The mechanism of pathogenicity in LRRC56 mutations is biallelic loss of function.

The gene-disease association between LRRC56 and PCD 39 is supported by gene expression data that show LRRC56 expression in ciliated tissues. GTEx RNA-seq expression studies in reference human tissues show strong expression of LRCC56 in lung, testis, brain, and Fallopian tube (PMID: 23715323). This pattern is consistent with the role that LRCC56 is thought to play in the assembly/transport of ODAs in motile cilia and flagella (sperm). Patients with LRRC56 related PCD also have laterality defects such as situs inversus and dextrocardia (may also have cardiac defects) suggesting dysfunction in the embryonic node motile cilia. A transcriptomic profile list of Left Right Organizer (LRO) genes from precisely staged 0–1 somite (when the LRO fluid flow is first detected) mouse embryos was generated using single cell RNA sequencing. LRRC56 was one of 196 transcripts described as part of the LRO transcriptome (PMID: 37393374). This nodal localization is consistent with the observation that LRRC56 mutations disrupt left-right patterning.

IFT is essential for the development and maintenance of motile and sensory cilia. The efficient transport of ODAs into cilia is mediated by the IFT system. Coimmunoprecipitation studies in HEK293 cells show an interaction between human LRRC56 and IFT88, one of at least 16 subunits that form the IFT-B protein complex (PMID: 30388400). In Trypanosoma brucei, LRRC56 is a transient cargo of IFT trains during flagellum construction (PMID: 38865178) suggesting that LRRC56 may associate with the IFT trains as a cargo adaptor to transport ODAs from the cytoplasm to the cilia compartment. LRRC56 also interacts with the distal docking complex (dDC) where ODAs are released to bind the dDC on the axoneme (PMID: 38865178). LRRC56 could play a role in the transport or unloading and attachment of dDC to the axoneme.

Two non-human experimental models have been used to support the gene-disease relationship between LRRC56 and PCD 39. LRRC56 knockout in Trypanosoma brucei results in a reduction in flagellar beating and cell swimming as well as an erratic swimming pattern. TEM studies show a reduction in ODAs, and immunofluorescent studies show that this reduction is mostly in the distal tip of the flagellum (PMID: 30388400). A functional alteration was also seen in trypanosomes carrying a missense LRRC56 human variant (LRRC56:c.419T>C p.L140P) seen in one of the fetal probands as a homozygous mutation. These mutants show reduced motility and a reduction in ODAs (PMID: 30388400). A Chlamydomonas reinhardtii null mutant, oda8, is characterized by the absence of ODAs all along the axoneme, reduced flagellar beat frequency, and impaired motility (slow swimming) (PMID: 2974040). The expression of ODA8 (LRRC56) restores wild type phenotype in these cells (PMID: 25558044). Of note: Mutations or deletion of the LRRC56 gene lead to reduced ciliary motility in all species investigated so far, but with variable impact on ODA presence. The ODA defects seen in LRRC56 loss of function mutations in trypanosome and Chlamydomonas have not been seen in human patients, although there is evidence of ciliary impairment in patients (PMID:30388400). There are no published mammalian model systems that might further support an understanding of the LRRC56-PCD relationship and provide insight to the mechanism of LRRC56 dysfunction in human patients.

In summary, there is moderate evidence supporting a gene-disease relationship between variants in LRCC56 and Primary Ciliary Dyskinesia 39. This classification was approved by the ClinGen Motile Ciliopathy GCEP on September 19, 2024 (SOP Version 11).