ClinVar Genomic variation as it relates to human health

Observed in patients with Stargardt disease in published literature who were reported to have V1433I on the same allele (in cis) with other ABCA4 variants or seen phase unknown with two other pathogenic ABCA4 variants, therefore questioning the pathogenicity of V1433I (Klevering et al., 2004; Lambertus et al., 2016; Murro et al., 2017; Birtel et al., 2018); In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 22995991, 34073554, 22025579, 27527345, 28002570, 28430335, 34426522, 20981092, 35119454, 29555955, 33090715, 15494742, 28341476, 32037395, 24409374, 22264887, 9973280)

ABCA4: PM1

The ABCA4 variant c.4297G>A; p.Val1433Ile (rs56357060) is reported in the medical literature in individuals with ABCA4-related disease as well as age related macular degeneration in the compound heterozygous state in a few individuals, but often without an additional pathogenic variant (Aguirre-Lamban 2009, Klevering 2004, Lewis 1999, Michaelides 2007, Song 2011, Souied 2000, Taylor 2017, Thiadens 2012, Webster 2001). The variant is reported in the ClinVar database (Variation ID: 99274) and in the Genome Aggregation Database in the general population with an allele frequency of 0.2% (470/282886 alleles including 1 homozygote). The amino acid at this position is highly conserved but computational algorithms (PolyPhen-2, SIFT) predict this variant is tolerated. Considering available information, there is insufficient evidence to classify this variant with certainty. References: Aguirre-Lamban J et al. Molecular analysis of the ABCA4 gene for reliable detection of allelic variations in Spanish patients: identification of 21 novel variants. Br J Ophthalmol. 2009 May;93(5):614-21. Klevering BJ et al. Three families displaying the combination of Stargardt's disease with cone-rod dystrophy or retinitis pigmentosa. Ophthalmology. 2004 Mar;111(3):546-53. Lewis RA et al. Genotype/Phenotype analysis of a photoreceptor-specific ATP-binding cassette transporter gene, ABCR, in Stargardt disease. Am J Hum Genet. 1999 Feb;64(2):422-34. Michaelides M et al. ABCA4 mutations and discordant ABCA4 alleles in patients and siblings with bull's-eye maculopathy. Br J Ophthalmol. 2007 Dec;91(12):1650-5. Song J et al. High-throughput retina-array for screening 93 genes involved in inherited retinal dystrophy. Invest Ophthalmol Vis Sci. 2011 Nov 25;52(12):9053-60. Souied EH et al. ABCR gene analysis in familial exudative age-related macular degeneration. Invest Ophthalmol Vis Sci. 2000 Jan;41(1):244-7. Taylor RL et al. Panel-Based Clinical Genetic Testing in 85 Children with Inherited Retinal Disease. Ophthalmology. 2017 Jul;124(7):985-991. Thiadens AA et al. Clinical course, genetic etiology, and visual outcome in cone and cone-rod dystrophy. Ophthalmology. 2012 Apr;119(4):819-26 Webster AR et al. An analysis of allelic variation in the ABCA4 gene. Invest Ophthalmol Vis Sci. 2001 May;42(6):1179-89.

The ABCA4 p.Val1433Ile variant was identified in 9 of 1492 proband chromosomes (frequency: 0.006) from individuals or families with stargardt disease, cone-rod dystrophy, age-related macular degeneration and retinitis pigmentosa (Schulz_2017_PMID:28118664; Thiadens_2012_PMID:22264887; Aguirre-Lamban_2009_PMID:19028736; Baum_2003_PMID:12592048; Lewis_1999_PMID:9973280). The variant was identified in dbSNP (ID: rs56357060), ClinVar (classified as likely pathogenic by Institute of Human Genetics, Univ. Regensburg and as a VUS by EGL Genetic Diagnostics and Illumina) and in LOVD 3.0 (classified as pathogenic once, a VUS four times and likely benign twice). The variant was also identified in control databases in 470 of 282886 chromosomes (1 homozygous) at a frequency of 0.001661 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 322 of 129192 chromosomes (freq: 0.002492), Other in 14 of 7226 chromosomes (freq: 0.001937), East Asian in 35 of 19952 chromosomes (freq: 0.001754), Latino in 56 of 35440 chromosomes (freq: 0.00158), European (Finnish) in 19 of 25118 chromosomes (freq: 0.000756), African in 16 of 24972 chromosomes (freq: 0.000641), South Asian in 7 of 30616 chromosomes (freq: 0.000229), and Ashkenazi Jewish in 1 of 10370 chromosomes (freq: 0.000096). The p.Val1433 residue is conserved in mammals but not in more distantly related organisms however four out of five computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) do not suggest a high likelihood of impact to the protein; this information is not predictive enough to rule out pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. 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.4297G>A variant is predicted to result in the amino acid substitution p.Val1433Ile. This variant has been reported in the heterozygous state alone or with a second ABCA4 variant in individuals with Stargardt disease and cone-rod dystrophy (for example, see Lewis et al. 1999. PubMed: 9973280; Thiadens et al. 2012. PubMed: 22264887; Taylor et al. 2017. PubMed ID: 28341476; Del Pozo-Valero et al. 2022. PubMed ID: 35119454). Of note, this variant has also been detected in an individual who also had a potential causative variant in the PROM1 gene (associated with a retinal disorder) (Song et al. 2011. PubMed: 22025579). However, this variant is reported in 0.25% of alleles in individuals of European (Non-Finnish) descent in gnomAD, including in several homozygous individuals in the latest gnomAD dataset (https://gnomad.broadinstitute.org/variant/1-94030483-C-T?dataset=gnomad_r4), which may be too common to be a primary cause of disease. Although we suspect that this variant may be benign, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.