ClinVar Miner

Submissions for variant NM_000350.3(ABCA4):c.6089G>A (p.Arg2030Gln) (rs61750641)

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Total submissions: 14
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000085787 SCV000230645 pathogenic not provided 2016-08-10 criteria provided, single submitter clinical testing
Institute of Human Genetics, Univ. Regensburg,Univ. Regensburg RCV000178545 SCV000281948 likely pathogenic Stargardt disease 1 2016-01-01 criteria provided, single submitter clinical testing
GeneDx RCV000085787 SCV000329050 pathogenic not provided 2021-07-20 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Published functional studies demonstrate a mild damaging effect (Curtis et al., 2020); This variant is associated with the following publications: (PMID: 32467599, 27535533, 32845050, 31456290, 30798147, 30215852, 30718709, 23891399, 29555955, 18854780, 26103963, 24265693, 24713488, 28118664, 28044389, 27820952, 27596865, 11379881, 11527935, 27491360, 9973280, 25283059, 28559085, 29925512)
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000085787 SCV000883316 likely pathogenic not provided 2017-06-02 criteria provided, single submitter clinical testing The ABCA4 c.6089G>A;p.Arg2030Gln variant has been published in several individuals with Stargardt disease and other ABVA4-related disorders (Bertelsen 2014, Cideciyan 2005, Duncker 2015, Jaakson 2003, Lewis 1999, Webster 2001, Zhang 2015). However, the variant has also been published on the same allele as another pathogenic variant, p.Met1Val (Eisenberger 2013, Maia-Lopes 2009). The variant is listed in the ClinVar database (Variation ID: 99428) and the dbSNP variant database (rs61750641) with an allele frequency of 0.0615 percent (8/12998 alleles) in the Exome Variant Server and 0.03609 percent (100/277108 alleles) in the Genome Aggregation Database. The amino acid at this position is highly conserved across species, occurs in a transporter domain, and computational algorithms (PolyPhen2, SIFT) predict this variant is deleterious. Considering available information, this variant is classified as likely pathogenic. This variant would be causative for autosomal recessive Stargardt disease and other ABCA4-related disorders (OMIM#601691). References: Bertelsen M et al. Generalized choriocapillaris dystrophy, a distinct phenotype in the spectrum of ABCA4-associated retinopathies. Invest Ophthalmol Vis Sci. 2014 Apr 29;55(4):2766-76. Cideciyan AV et al. ABCA4-associated retinal degenerations spare structure and function of the human parapapillary retina. Invest Ophthalmol Vis Sci. 2005 Dec;46(12):4739-46. Duncker T et al. Quantitative fundus autofluorescence distinguishes ABCA4-associated and non-ABCA4-associated bull's-eye maculopathy. Ophthalmology. 2015 Feb;122(2):345-55. Eisenberger T et al. Increasing the yield in targeted next-generation sequencing by implicating CNV analysis, non-coding exons and the overall variant load: the example of retinal dystrophies. PLoS One. 2013 Nov 12;8(11):e78496. Jaakson K et al Genotyping microarray (gene chip) for the ABCR (ABCA4) gene. Hum Mutat. 2003 Nov;22(5):395-403. 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. Maia-Lopes S et al. ABCA4 mutations in Portuguese Stargardt patients: identification of new mutations and their phenotypic analysis. Mol Vis. 2009;15:584-91. Webster AR et al. An analysis of allelic variation in the ABCA4 gene. Invest Ophthalmol Vis Sci. 2001 May;42(6):1179-89. Zhang Q et al. Next-generation sequencing-based molecular diagnosis of 35 Hispanic retinitis pigmentosa probands. Sci Rep. 2016 Sep 6;6:32792.
Fulgent Genetics,Fulgent Genetics RCV000763436 SCV000894203 likely pathogenic Cone-rod dystrophy 3; Age-related macular degeneration 2; Stargardt disease 1; Retinitis pigmentosa 19 2018-10-31 criteria provided, single submitter clinical testing
Invitae RCV000085787 SCV001214008 pathogenic not provided 2020-10-09 criteria provided, single submitter clinical testing This sequence change replaces arginine with glutamine at codon 2030 of the ABCA4 protein (p.Arg2030Gln). The arginine residue is highly conserved and there is a small physicochemical difference between arginine and glutamine. This variant is present in population databases (rs61750641, ExAC 0.06%). This variant has been observed on the opposite chromosome (in trans) from other pathogenic variants in individuals affected with Stargardt disease (PMID: 23143460, 22229821). This finding is consistent with autosomal recessive inheritance, and suggests that this variant contributes to disease. ClinVar contains an entry for this variant (Variation ID: 99428, 236068). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. For these reasons, this variant has been classified as Pathogenic.
Blueprint Genetics RCV001074874 SCV001240478 pathogenic Retinal dystrophy 2019-08-08 criteria provided, single submitter clinical testing
CeGaT Praxis fuer Humangenetik Tuebingen RCV000085787 SCV001247597 pathogenic not provided 2020-01-01 criteria provided, single submitter clinical testing
Centre for Mendelian Genomics,University Medical Centre Ljubljana RCV001197157 SCV001367793 pathogenic Age-related macular degeneration 2 2018-11-23 criteria provided, single submitter clinical testing This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PM1,PP2,PP3,PP5.
Retina International RCV000085787 SCV000117929 not provided not provided no assertion provided not provided
Medical Genetics Laboratory, Kennedy Center,Juliane Marie Center, Rigshospitalet RCV000787516 SCV000926484 pathogenic Vitreoretinopathy 2018-04-01 no assertion criteria provided research
Medical Genetics Laboratory, Kennedy Center,Juliane Marie Center, Rigshospitalet RCV000787517 SCV000926485 pathogenic Macular dystrophy 2018-04-01 no assertion criteria provided research
Medical Genetics Laboratory, Kennedy Center,Juliane Marie Center, Rigshospitalet RCV000787766 SCV000926771 pathogenic Progressive cone dystrophy (without rod involvement) 2018-04-01 no assertion criteria provided research
Human Genetics - Radboudumc,Radboudumc RCV000085787 SCV001955238 likely pathogenic not provided no assertion criteria provided clinical testing

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