The NM_000350.3(ABCA4):c.32T>C variant in ABCA4 is a missense variant predicted to cause substitution of leucine by proline at amino acid 11 (p.Leu11Pro). The total minor allele frequency in gnomAD v4.1.0 is 0.000004337 (7/1613874 alleles), which is lower than the ClinGen ABCA4 VCEP’s threshold for PM2_Supporting (<0.0001), meeting this criterion (PM2_Supporting). The computational predictor REVEL gives a score of 0.948 which is above the threshold of >0.772, evidence that predicts a damaging effect on ABCA4 function (PP3_Moderate). The prevalence of the variant in affected individuals is significantly increased compared with the prevalence in controls with an OR of 95.5 and the CI is 12.78-41149.08, which is above the ABCA4 VCEP threshold of ≥5, where the CI does not contain 1 (PS4; PMID: 35120629). This variant has been detected in at least 2 individuals with ABCA4-related retinopathy who were compound heterozygotes for the variant and a pathogenic variant (c.1A>G; p.Met1Val, c.2888delG) and both of those were confirmed in trans by family testing (PM3_Strong; PMIDs: 19365591, 17325136). In summary, this variant meets the criteria to be classified as pathogenic for ABCA4-related retinopathy based on the ACMG/AMP criteria applied, as specified by the ClinGen ABCA4 VCEP (Specification Version 1.0): PS4, PM3_Strong, PM2_Supporting, PP3_Moderate.

This sequence change replaces leucine, which is neutral and non-polar, with proline, which is neutral and non-polar, at codon 11 of the ABCA4 protein (p.Leu11Pro). This variant is present in population databases (rs62645946, gnomAD 0.0009%). This missense change has been observed in individual(s) with ABCA4-related conditions (PMID: 17325136, 19365591, 29925512, 30093795). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 99217). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is expected to disrupt ABCA4 protein function with a positive predictive value of 95%. For these reasons, this variant has been classified as Pathogenic.

The ABCA4 c.32T>C (p.Leu11Pro) missense variant has been reported in at least six studies in which it is found in a total of eight individuals, including in a compound heterozygous state in six subjects diagnosed with Stargardt disease (STGD), and in a heterozygous state in one individual with STGD and one with late onset fundus flavimaculatus (Rozet et al. 1998; Valverde et al. 2007; Maia-Lopes et al. 2009; Riveiro-Alvarez et al. 2013; Salles et al. 2018). The p.Leu11Pro variant was absent from 110 healthy controls and is reported at a frequency of 0.000015 in the European (non-Finnish) population of the Exome Aggregation Consortium, but this is based on one allele so the variant is presumed to be rare. Based on the evidence the p.Leu11Pro variant is classified as pathogenic for ABCA4-related disorders. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.

The p.Leu11Pro variant in ABCA4 was identified in an individual with Retinitis pigmentosa, via a collaborative study between the Broad Institute's Center for Mendelian Genomics and the Pierce lab (https://oculargenomics.meei.harvard.edu/labs/pierce-lab/lab-members/). Through a review of available evidence we were able to apply the following criteria: PM2, PP3, PM3-S. Based on this evidence we have classified this variant as Likely Pathogenic. If you have any questions about the classification please reach out to the Pierce Lab.

Clinical significance based on ACMG v2.0

Clinical significance based on ACMG v2.0

The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.000%). Predicted Consequence/Location: Missense variant Functional studies provide moderate evidence of the variant having a damaging effect on the gene or gene product (PMID: 17325136). In silico tool predictions suggest damaging effect of the variant on gene or gene product [REVEL: 0.95 (>=0.6, sensitivity 0.68 and specificity 0.92); 3Cnet: 0.69 (>=0.6, sensitivity 0.72 and precision 0.9)]. Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000099217 /PMID: 9781034).The variant has been reported to be in trans with a pathogenic variant as either compound heterozygous or homozygous in at least 4 similarly affected unrelated individuals (PMID: 17325136, 19365591, 29925512, 30093795). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline.

PS4, PM2_P, PM3_S, PP3_M

NM_000350.3(ABCA4):c.32T>C (p.Leu11Pro) is a missense variant that results in the substitution of leucine with proline. Segregation evidence has been reported in affected families. This variant has been observed in affected individuals with Retinitis pigmentosa 40 in a genotype context consistent with recessive disease (PMID: 17325136; PMID: 19365591; PMID: 29925512; PMID: 30093795; PMID: 32619608). This variant has been recurrently observed in individuals with Retinitis pigmentosa 40 (PMID: 17325136; PMID: 19365591; PMID: 29925512; PMID: 30093795; PMID: 32619608). Multiple computational predictions support a deleterious effect on the gene or gene product. The variant is present at low frequency in population datasets. Based on the available data, this variant is classified as pathogenic.