ClinVar Genomic variation as it relates to human health

The ABCA4 c.6148G>C; p.Val2050Leu variant (rs41292677) is reported in the literature in multiple individuals affected with Stargardt disease, retinitis pigmentosa, or a related retinal disorder (Allikmets 1997, Corton 2013, Haer-Wigman 2017, Sciezynska 2016, Wiszniewski 2005). This variant has been observed in trans to a pathogenic variant in affected individuals (Corton 2013); however, it has also been observed in cis to a nonsense variant in at least one study (Sciezynska 2016). The p.Val2050Leu variant is found in the Latino population with an overall allele frequency of 0.60% (211/35438 alleles) in the Genome Aggregation Database and is reported with conflicting classifications in ClinVar (Variation ID: 7884). The leucine at codon 2050 is highly conserved, but computational analyses (SIFT: tolerated, PolyPhen-2: damaging) predict conflicting effects of this variant on protein structure/function. Due to conflicting information, the clinical significance of the p.Val2050Leu variant is uncertain at this time. References: Allikmets R et al. A photoreceptor cell-specific ATP-binding transporter gene (ABCR) is mutated in recessive Stargardt macular dystrophy. Nat Genet. 1997 Mar;15(3):236-46. Corton M et al. Exome sequencing of index patients with retinal dystrophies as a tool for molecular diagnosis. PLoS One. 2013 Jun 14;8(6):e65574. Haer-Wigman L et al. Diagnostic exome sequencing in 266 Dutch patients with visual impairment. Eur J Hum Genet. 2017 May;25(5):591-599. Sciezynska A et al. Next-generation sequencing of ABCA4: High frequency of complex alleles and novel mutations in patients with retinal dystrophies from Central Europe. Exp Eye Res. 2016 Apr;145:93-99. Wiszniewski W et al. ABCA4 mutations causing mislocalization are found frequently in patients with severe retinal dystrophies. Hum Mol Genet. 2005 Oct 1;14(19):2769-78.

Across a selection of available literature, the ABCA4 c.6148G>C (p.Val2050Leu) missense variant has been reported in at least seven individuals affected with Stargardt macular degeneration including in three in a compound heterozygous state, in one in a heterozygous state and in at least three with unknown zygosity. The variant has also been reported in two brothers affected with cone-rod dystrophy in a compound heterozygous state with a frameshift variant on the second allele, and in a heterozygous state in one individual affected with macular dystrophy (Allikmets et al. 1997; Lewis et al. 1999; Corton et al. 2013; Schulz et al. 2017; Haer-Wigman et al. 2017). The variant failed to segregate with the disorder in one family affected with autosomal recessive retinitis pigmentosa and in one with autosomal dominant macular dystrophy (Wiszniewski et al. 2005; Poloschek et al. 2010). The p.Val2050Leu variant has also been found as a complex allele in cis with either a stop-gained variant or a missense variant in individuals affected with ABCA4-related disorders (Sciezynska et al. 2016; Schulz et al. 2017). The variant was found in a heterozygous state in one of 1528 control individuals and in one unaffected parent (Allikmets et al. 1997; Lewis et al. 1999; Corton et al. 2013; Sciezynska et al. 2016). This variant is reported at a frequency of 0.028846 in Puerto Ricans from Puerto Rico from the 1000 Genomes Project and in one homozygote in the European (non-Finnish) population of the Genome Aggregation Database. Poloschek et al. (2010) showed that, upon ophthalmic examination, heterozygous carriers of the p.Val2050Leu variant display centrally reduced mfERG amplitudes and additional minor fundus abnormalities, suggesting that the p.Val2050Leu variant is capable of mildly reducing macular function in the heterozygous state without an additional pathogenic variant on the second allele. Based on the collective evidence the p.Val2050Leu variant is classified as a variant of unknown significance but suspicious for pathogenicity for ABCA4-related disorders. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as VUS-3B. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with ABCA4-related eye disease (OMIM). (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0115 - Variants in this gene are known to have variable expressivity (PMID: 31522899) . (I) 0200 - Variant is predicted to result in a missense amino acid change from valine to leucine. (I) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD <0.01 for a recessive condition (v3) (468 heterozygotes, 2 homozygotes). (SP) 0502 - Missense variant with conflicting in silico predictions and uninformative conservation. (I) 0600 - Variant is located in the annotated ABC transporter domain (PDB). (I) 0705 - No comparable missense variants have previous evidence for pathogenicity. (I) 0809 - Previous evidence of pathogenicity for this variant is inconclusive. This variant has been reported as benign, likely benign, likely pathogenic and as a VUS six times in ClinVar (most recently benign and VUS). It has been reported as a homozygous variant in at least one patient with macular dystrophy with no additional data (PMID: 31736247) and in trans with another pathogenic missense variant in a retinitis pigmentosa family however segregation data was inconclusive (PMID: 25698705). This variant has also been reported as a heterozygous variant in multiple patients with ABCA4-related eye disease, where a 2nd disease-causing variant was not determined (PMID 22427542; 23755871; 30190494; 30718709). In addition, this variant has been identified as a complex allele with unknown zygosity in at least 2 families (PMID: 32783370; 30060493). (I) 1007 - No published functional evidence has been identified for this variant. (I) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

Observed in patients with Stargardt disease and retinal dystrophy in the presence of another ABCA4 variant, but also in the heterozygous state in individuals with a pathogenic variant in another gene explaining their phenotype (PMID: 23940504, 25698705, 28118664, 28061825, 29555955, 29884405, 29925512, 30718709); Observed in the homozygous state in a patient with macular dystrophy in the literature (PMID: 31736247); In silico analysis indicates that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 1137988, 22427542, 31429209, 32531858, 25698705, 9054934, 9666097, 16103129, 23953153, 15494742, 11726554, 9973280, 11527935, 18285826, 28224992, 26593885, 34426522, 33546218, 12796258, 28118664, 25884411, 28061825, 10913642, 29555955, 28492530, 11328725, 28341476, 30190494, 30798147, 29884405, 28157192, 30653986, 30718709, 31212395, 30670881, 31980526, 32581362, 32619608, 32783370, 23940504, 29925512, 33633436, 35836572, 34327195, 34996991, 31736247, 37958660, 35120629, 30060493, 28041643, 23755871, 36969552, 36010202, 36209838, 10880298, 20335603)

ABCA4: BP2, BS2

The ABCA4 p.Val2050Leu variant was identified in 13 of 2830 proband chromosomes (frequency: 0.00459) from individuals or families with inherited retinal diseases including macular dystrophy, cone-rod dystrophy and Stargardt disease (Haer-Wigman_2017_PMID:28224992; Carss_2017_PMID:28041643; Schulz_2017_PMID:28118664; Sciezynska_2016_PMID:26593885). A study of a family with macular dystrophy, cone dystrophy, and cone–rod dystrophy in five-generations identified variants in the PRPH2, ABCA4, and ROM1 genes; family members heterozygous for only the ABCA4 V2050L variant showed mildly reduced macular function with centrally reduced mfERG amplitudes and additional minor fundus abnormalities (Poloschek_2010_PMID:20335603). The V2050L variant was identified in dbSNP (ID: rs41292677), ClinVar (classified as benign 1x, likely benign 4x, VUS 2x, likely pathogenic 2x and pathogenic 1x) and LOVD 3.0 (classified as a VUS and likely pathogenic). The variant was also identified in control databases in 808 of 282834 chromosomes (1 homozygous) at a frequency of 0.002857 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: Latino in 211 of 35438 chromosomes (freq: 0.005954), Ashkenazi Jewish in 50 of 10368 chromosomes (freq: 0.004823), Other in 29 of 7226 chromosomes (freq: 0.004013), European (non-Finnish) in 500 of 129166 chromosomes (freq: 0.003871), African in 13 of 24950 chromosomes (freq: 0.000521) and European (Finnish) in 5 of 25118 chromosomes (freq: 0.000199); it was not observed in the East Asian or South Asian populations. The p.Val2050 residue is 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. The p.Val2050Leu variant occurs in the first base of the exon; this position has been shown to be part of the splicing consensus sequence and variants involving this position sometimes affect splicing. However, only 2 of 4 in silico or computational prediction software programs (MaxEntScan, GeneSplicer) predict a greater than 10% 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.6148G>C variant is predicted to result in the amino acid substitution p.Val2050Leu. This variant has been reported in several large cohort studies of retinal disease; however, often times a second ABCA4 variant was not detected (see for examples: Corton et al. 2013. PubMed ID: 23940504; Wiszniewski et al. 2005. PubMed ID: 16103129; Poloschek et al. 2010. PubMed ID: 20335603; Table S1, Lin et al. 2024. PubMed ID: 38219857 ). This variant is reported in 0.60% of alleles in individuals of Latino descent in gnomAD, including several homozygous individuals in the latest dataset (https://gnomad.broadinstitute.org/variant/1-94001992-C-G?dataset=gnomad_r4). 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.