The work intersects clinical genetics, retinal dystrophy and variant interpretation, delivering guidance for clinical reporting and strengthening the evidence that CERKL is also a contributor to inherited retina dystrophy. To date, data on the prevalence of autosomal-recessive retinal dystrophies in the Brazilian population are scarce; specifically, for CERKL, this is the first report to describe a genotype-phenotype correlation. This paper may contribute to increase the knowledge of populational data and understanding the genetic bases in a diverse ethnic population. We believe this will interest clinicians and researchers working on retina degeneration and gene-level mechanisms.

Inherited retinal dystrophies (IRD) are a heterogenous group of ocular diseases characterized by progressive photoreceptor degeneration due to apoptosis, leading to irreversible blindness. Retinitis pigmentosa (RP; MIM 268000) is the most common IRD; more than ninety genes have been implicated in the autosomal-recessive form to date [1]. Cone-rod dystrophy (CORD) is a rarer IRD, with an estimated prevalence of approximately 1:40,000 in Europe [2]. Unlike typical RP, CORD is characterized by primary cone dysfunction followed by secondary rod degeneration [3]. Classical clinical features include progressive loss of central vision, color-vision disturbance, and photophobia, followed by nyctalopia and peripheral field constriction. Overall, CORD tends to progress more rapidly and patients reach legal blindness earlier than those with retinitis pigmentosa.

CERKL-related retinopathy (MIM 608380), recorded as RP26 in OMIM, accounts for an estimated 4–7% of autosomal-recessive IRD cases across diverse populations [4–6]. In founder populations, the proportion can be substantially higher, up to 33% in specific cohorts due to founder effects [7–11].

Ceramide kinase-like (CERKL) gene has been first mapped in chromosome 2q31.2-q32 in a consanguineous Spanish family with autosomal recessive RP (arRP) in 1998 [12]. A few years later, Tuson and colleagues identified a homozygous mutation in exon 5 of CERKL in this same Spanish family and in an additional unrelated family [7]. This report was the first to provide evidence suggesting a link between retinal degeneration in RP and sphingolipid-mediated apoptosis. The CERKL gene shows higher transcription levels in the retina and is also expressed in other tissues, including the brain, lung, and kidney [13].

To date, data on the prevalence of autosomal-recessive retinal dystrophies in the Brazilian population are scarce; specifically, for CERKL, this is the first report to describe a genotype–phenotype correlation.

Using the transcript NM_001030311 as the reference, CERKL comprises 14 exons and encodes a 558 amino acid protein. This isoform comprises a diacylglycerol kinase domain (DAGK) and a putative N-terminal pleckstrin homology (PH) region.¹³ Different retinal isoforms produce multiple transcripts as a result of alternative splicing [14].

CERKL genes show 29% identity and 50% similarity with the human ceramide kinase (CERK) protein [15] which participates in oxidative stress protection, but no kinase activity was shown [16]. The exact role of CERKL remains unclear. A recent study using a CERKL knockdown mouse model, generated by CRISPR-based gene silencing, demonstrated an inability to activate cell protection upon light stress conditions [17]. CERKL is a resilience gene in oxidative stress; therefore, altered expression may trigger retinal degeneration through apoptosis and non-apoptotic inflammatory response mediated by glia.

Ceramide is a sphingolipid that has a central role in lipid metabolism, both structural for the lipid cell membrane composition and metabolic. Ceramide acts as a signaling lipid in multiple cellular pathways that regulate cell growth, cell differentiation, senescence, and apoptosis. Ceramide level increase or imbalance triggers photoreceptor degeneration, induces amacrine cell death, and contributes to retinal pigmented epithelial (RPE) cell dysfunction and atrophy.

Sphingosine (Sph) is an 18-carbon, long chain amino alcohol, the canonical sphingoid base d18:1, that serves as the common backbone of most sphingolipids. The ceramide structure is formed by n-acylation of sphingosine with fatty acid, creating an amid bond, N-acylsphingosine. Figure 1 displays how sphingolipid intermediate metabolites and ceramides are interconnected in a network.

The clinical notes of 2841 Brazilian patients diagnosed with IRD registered at Instituto de Genética Ocular between January 2006 and July 2025 were reviewed, from which fifty-seven patients with genetic testing suggestive of CERKL-related inherited retinal disease (IRD) were identified. Four patients were excluded due to missing clinical information. One patient, listed as 45.1 and identified as homozygous for a variant of uncertain significance (VUS), was excluded from the analysis. Data were obtained from clinicians’ notes detailing ophthalmological exams performed by specialists in IRD. Molecular test results were collected and analyzed for genotype-phenotype correlation. Ethical approval was provided by the Research Ethics Committee of Federal University of São Paulo (number 1191/2018) and the study complied with the tenets of the Declaration of Helsinki. When the DNA samples were collected for molecular tests, all patients and/or their legal guardians provided written informed consent for the use of their personal medical data for scientific purposes and publication.

Clinical data included detailed ocular examination findings, presenting signs and symptoms, age at disease onset, Snellen best corrected visual acuity (BCVA) measured at first visit, which was converted to log Mar [18, 19], slit-lamp biomicroscopy, fundus examination, digital color fundus picture, and, if available, fundus autofluorescence, spectral domain optical coherence tomography, and electrophysiological test. Phenotype classification was based primarily on clinical data and fundus picture analysis performed by specialists in IRD.

CERKL variants were identified by the panel sequencing of genes associated with inherited retinal disease performed in different laboratories using panel-based targeted next-generation sequencing (NGS) or whole-exome sequencing. The pathogenicity of variants was determined by the American College of Medical Genetics (ACMG) and the Association for Molecular Pathology (AMP) criteria [20]. Novel variants were classified as pathogenic or likely pathogenic according to the criteria of effect in the protein structure (frameshift or nonsense of copy number variation or affecting a canonical splice site), frequency in the gnomAD population database, and classification by pathogenic predictors. Two platforms were assessed to assist variant interpretation, namely Franklin (https://franklin.genoox.com) and Varsome (https://varsome.com), assessed on 4 Sep 2025. Variants found in the cohort were compared with the listed ones in Clin Var Nucleotide (https://www.ncbi.nlm.nih.gov/clinvar/assessed on 4 Sep 2025), and protein numbering is based on CERKL transcript NM_01030311 (Figure 2). Owing to the retrospective design of the study and the lack of available parental specimens, segregation analysis was not performed for any of the families in this cohort.

CERKL is an ultrarare gene implicated in IRD in different ethnic populations [7, 21–24]. In this Brazilian cohort, the CERKL gene accounts for 2% of the total positive tests for IRD, which is consistent with the 2.5% from a previous publication from our group [25] in 2018.

The relative frequency rates in diverse IRD in Brazil are comparable and aligned with the 0.72% reported in the global pool from the Foundation Fighting Blindness Clinical Consortium [26], which corroborates that CERKL is an uncommon contributor to IRD.

Linear regression analysis was performed to evaluate the association between disease duration and visual acuity in CERKL-related retinal dystrophy patients, stratified by genotypic severity into double-null (DN) — carrying two loss-of-function alleles — and non-double-null (NDN) groups.

The analysis indicates that complete biallelic loss of CERKL function is associated with a more rapid and statistically predictable decline in visual acuity compared to the group retaining residual protein function.

The most frequent variant found was the c.847 C>T nonsense variant, with an allele frequency of 55.67%. This variant, c.847C>T, was the first described in Spanish families by Bayes e Tuson and is the most frequent found in the literature [24]. The allele frequency was reported to be 88.9% in Spain and 76.5% in Portugal [27]. The relative high frequency of the c.847C>T variant in our cohort may be explained by historical records suggesting that immigration to Brazil predominantly originated from Portugal and Italy [28], confirmed by a publication regarding genetic ancestry in Brazilian population [29].

Patients with this homozygous and compound heterozygous variant presented clinically as cone rod dystrophy phenotype. Compound heterozygous variants also included two patients with macular dystrophy phenotype (patients 24.1 and 31.1), an uncommon description for CERKL-related retinopathy.

CERKL-related retinopathy can present as early as 7 years old with a median of 18 years, with decrease in central vision associated with nyctalopia symptoms, and an early drop in visual acuity. Clinically, an optic disc not severely impaired, peripapillary atrophy, sparse mottled pigmentation, and central atrophy were observed. Sparse mottled RPE abnormalities were observed in the CORD phenotype with more diffuse and dense pigmentation abnormalities in advanced cases. These evolutive presentations have been described by other authors for CERKL-related retinopathy [23, 27]. Early macular involvement as a key feature and concomitant involvement of both rods and cones in full-field ERG points to a CORD phenotype presentation documented in other publications [8, 12] for 847C>T and c.238+1G>A variants. Avila et al. described how most of the patients in the Finland cohort had juvenile unspecified macular dystrophy as their initial diagnosis, while two patients had Stargardt disease as the initial diagnosis, due to Stargardt-like phenotype. Studies in murine retina suggest CERKL is more highly expressed in cones compared to rods [14, 30]. This information also strengths our hypothesis that CERKL related-retinopathy manifest predominantly as CORD phenotype.

The macular phenotype was noted in 2 individuals in our cohort (patients 24.1 and 31.1), both of whom had heterozygous compound variants but lacked a conclusive molecular diagnosis.

Patient 24.1 is compound heterozygous for c.1576G>A, pAsp526Asn and c.237_238+13del, p.Gly80fs variants for CERKL with bilateral hyperautofluorescent. This finding was also described by two authors for CERKL compound heterozygous cases with c.375C>G and c.193G>T variants (Avila et al) and c.1393C>T and c.316C>A variants [31].

Patient 31.1 is a female proband who was compound heterozygous for c.1238-10T>G and deletion exon3 variant for CERKL. The exon 3 deletion variant was not previously reported in the Clinvar database. This variant disrupts a region corresponding to the N-terminal portion of the diacylglycerol catalytic domain, which is responsible for the protein integrity of kinase fold. This evidence could disestablish a clinically significant region of the protein [14, 17] and means it is likely to be disease-causing. This may represent a new variant; additional functional studies are required to confirm its status.

Electrophysiological assessment was scarce, with only 3/52 individuals having performed the exam. As no clear correlation between ERG findings and clinical data exists [24], retinal electrical activity profile analysis of all individuals of the cohort would clarify the comprehension of CERKL- related retinopathy phenotype. The most consistent hallmark is a concomitant and parallel progressive impairment of both rod and cone systems [8, 23, 27].

Twenty-four different variants were found in our cohort. The Brazilian population is highly diverse, probably because of multiple admixture events between Indigenous American, African, and European parental sources; this fact could explain why there were a significant number of different variants in this cohort. A recent publication from the DNABR project, an initiative of Brazilian government to map the genetic diversity of the Brazilian population, has sequenced thousands of Brazilian genomes and identified more than 8 million previously unknown single nucleotide variants (SNVs) not present in the main public datasets.

Regarding gene function, strong evidence was provided for mitochondrial localization of the CERKL protein in the mammalian retina, specifically the isoforms containing exon 5 [32]. Depletion of CERKL levels in knockdown/knockout mouse retinas were shown to increase autophagy, mitochondrial fragmentation, alteration of mitochondrial distribution, and dysfunction of mitochondrial-dependent bioenergetics and metabolism, issues related to mitochondrial metabolic pathways. These results suggest that the CERKL gene acts as a regulator of mitochondrial biology and metabolism with a retinal resilience role.

The phenotype of CERKL-related retinopathy is predominantly CORD with an early decrease in visual acuity. The macular dystrophy phenotype was found in 2 patients, both compound heterozygous for CERKL variants, and provided hypothesis-generating observations that could not provide a conclusive molecular diagnosis. In addition to OMIM classifying this gene as an RP IRD, we believe CERKL has CORD phenotype, in concordance with evidence described in the literature.