ClinVar Genomic variation as it relates to human health

The c.4685T>C (p.Ile1562Thr) variant has been described in three studies in which it is found in a compound heterozygous state in two individuals with Stargardt disease, a heterozygous state (with no additional variant identified) in a third individual with Stargardt disease, and in a heterozygous state in two individuals with macular degeneration (Allikmets et al. 1997; Testa et al. 2012; Fujinami et al. 2013). The variant was observed in six out of 1260 control alleles (Allikmets et al. 1997; Rivera et al. 2000; Testa et al. 2012) and is reported at a frequency of 0.00218 in the European (Non-Finnish) population of the Exome Aggregation Consortium. Functional studies by Shroyer et al. (2001) demonstrated that the p.Ile1562Thr variant results in a substantial reduction in the ATP-binding ability of the protein whilst expression levels are unaffected compared to wild-type. Based on the evidence, the p.Ile1562Thr variant is classified as a variant of unknown significance but suspicious for pathogenicity for ABCA4-related disorders.

The heterozygous p.Ile1562Thr variant in ABCA4 was identified by our study in the compound heterozygous state, with another VUS, in one individual with cone rod dystrophy. This variant has been identified in 0.1266% (351/277160) of chromosomes and 1 homozygote by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs1762111). Although this variant has been seen in the general population in the homozygous state, its frequency is low enough to be consistent with a recessive carrier frequency with a later age of onset. Please note that for diseases with clinical variability, or reduced penetrance, pathogenic variants may be present at a low frequency in the general population. Computational prediction tools and conservation analyses suggest that this variant may impact the protein. In vitro functional studies provide some evidence that the p.Ile1562Thr variant may impact protein function by lowering the ATP-binding affinity of the protein (PMID: 11726554). However, these types of assays may not accurately represent biological function. The p.Ile1562Thr variant in ABCA4 has been reported in one individual with cone rod dystrophy, but did not segregate with disease in an affected parent and sibling from the same family (PMID: 11726554). In summary, the clinical significance of the p.Ile1562Thr variant is uncertain. ACMG/AMP Criteria applied: PP3, PS3, BS4 (Richards 2015).

The p.Ile1562Thr variant in ABCA4 has been reported in at least 5 individuals with Stargardt disease in association with a second pathogneic or likely pathogenic variant. In addition, it has been identified in the heterozygous state without a clear second pathogenic variant in at least 1 individual with Stargardt disease and 2 individuals with macular degeneration (Allikmets 1997 PMID: 9295268; Testa 2012 PMID: 22661472; Fujinami 2013 PMID: 23953153, Downes 2012 PMID: 23143460. Sung 2019 PMID: 29975949, Lee 2022 PMID: 34874912). The observation of this variant in trans with a loss of function variant in individuals with a mild form of Stargardt disease suggests this variant might act as a hypomorph (Lee 2022 PMID: 34874912). This variant has been identified in 0.288% (10/3472) of Ashkenazi Jewish and in 0.22% (152/68026) of European chromosomes by gnomAD ( v3.1.2 (http://gnomad.broadinstitute.org), and in one homozygous individual in gnomAD (v2.1.1). Computational prediction tools and conservation analyses do not provide strong support for or against an impact to the protein. In vitro functional studies provide some evidence that this variant may impact protein function by lowering the ATP-binding affinity of the protein (Shroyer 2001 PMID: 11726554); however, these types of assays may not accurately represent biological function. In summary, while there is some suspicion for a pathogenic role, the clinical significance of this variant is uncertain. ACMG/AMP Criteria applied: PS3_Supporting, PM3_Strong

This sequence change replaces isoleucine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 1562 of the ABCA4 protein (p.Ile1562Thr). This variant is present in population databases (rs1762111, gnomAD 0.2%), including at least one homozygous and/or hemizygous individual. This missense change has been observed in individual(s) with Stargardt disease or cone-rod dystrophy, but there is no convincing evidence that it segregates with disease (PMID: 11527935, 22661472, 28041643, 29975949, 30718709, 35120629). ClinVar contains an entry for this variant (Variation ID: 99311). 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) has been performed for this missense variant. However, the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on ABCA4 protein function. Experimental studies have shown that this missense change affects ABCA4 function (PMID: 11726554). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

Published functional studies demonstrate that the variant reduces ATP-binding ability (PMID: 11726554); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 10958763, 11818392, 20849526, 9295268, 11379881, 35120629, 32581362, 25087612, 23953153, 23143460, 17982420, 15696369, 23982839, 33836713, 30718709, 29925512, 28118664, 28771251, 29555955, 28838317, 29068140, 29975949, 34426522, 34874912, 34945039, Lee[abstract]2021, 30834176, 11726554, 11527935, 36460718, 32531858, 31429209, 28041643)

ABCA4: PM3:Strong, PM2:Supporting, PS3:Supporting

The ABCA4 p.Ile1562Thr variant was not identified in the Cosmic or LOVD 3.0 databases. The variant was identified in dbSNP (ID: rs1762111), ClinVar (reported as uncertain signficance (5), pathogenic and likely pathogenic), Clinvitae and MutDB. The variant was identified in control databases in 353 of 282818 chromosomes (1 homozygous) at a frequency of 0.001248 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: European (non-Finnish) in 283 of 129140 chromosomes (freq: 0.002191), Other in 14 of 7228 chromosomes (freq: 0.001937), Ashkenazi Jewish in 17 of 10364 chromosomes (freq: 0.00164), European (Finnish) in 20 of 25124 chromosomes (freq: 0.000796), South Asian in 7 of 30614 chromosomes (freq: 0.000229), Latino in 8 of 35432 chromosomes (freq: 0.000226) and African in 4 of 24964 chromosomes (freq: 0.00016); it was not observed in the East Asian population. The p.I1562T variant was identified in 1/79 compound heterozygous patients with ABCA4-associated diseases, however was suggested to be benign (Fujinami_2013_PMID: 23982839). Downes et al. (2012) identified the variant in a patient with bull's eye maculopathy who also had an affected parent and sibling, however the I1562T variant was not found to cosegregate with disease (Downes_2012_PMID: 23143460). The variant was also identified in 3/335 patients with Stargardt disease and predicted to be pathogenic (Schulz_2017_PMID: 28118664). The p.Ile1562 residue is not conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the impact to the protein; this information is not very predictive of pathogenicity. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.

The ABCA4 c.4685T>C variant is predicted to result in the amino acid substitution p.Ile1562Thr. This variant has been reported in multiple individuals with ABCA4-related retinal disease (Allikmets et al. 1997. PubMed ID: 9295268; Downes et al. 2012. PubMed ID: 23143460). It has been proposed to be a mild variant (Table S2, Cornelis et al. 2022. PubMed ID: 35120629). This variant is reported in 0.22% of alleles in individuals of European (Non-Finnish) descent in gnomAD. Although we suspect that this variant may be pathogenic, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.