NM_000350.3:c.5882G>A
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 12P and 2B. PM1PM5PP5_Very_StrongBP4BS1_Supporting
The NM_000350.3(ABCA4):c.5882G>A(p.Gly1961Glu) variant causes a missense change. The variant allele was found at a frequency of 0.00341 in 1,614,012 control chromosomes in the GnomAD database, including 44 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic low penetrance (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G1961R) has been classified as Likely pathogenic.
Frequency
Consequence
NM_000350.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes 0.00311 AC: 473AN: 152092Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.00470 AC: 1181AN: 251452Hom.: 9 AF XY: 0.00537 AC XY: 730AN XY: 135906
GnomAD4 exome AF: 0.00344 AC: 5025AN: 1461802Hom.: 41 Cov.: 31 AF XY: 0.00384 AC XY: 2792AN XY: 727210
GnomAD4 genome 0.00311 AC: 473AN: 152210Hom.: 3 Cov.: 32 AF XY: 0.00321 AC XY: 239AN XY: 74422
ClinVar
Submissions by phenotype
Severe early-childhood-onset retinal dystrophy Pathogenic:19Other:1
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This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868]. -
Variant is located in a mutational hotspot where >50% of variants are pathogenic (PM1). Other variant at this amino acid residue has been classified as pathogenic (PM5, p.Gly1961Arg). REVEL score is 0.76 (PP3). Study has shown the variant affects the function of the protein (PS3_sup, PMID:29847635). Cosegregation with disease has been observed in multiple families in multiple studies (PP1_str, PMID:20696155;16103129;19217903;19074458) -
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PM3_VeryStrong+PP4+PM2_Supporting+PM5+PP3 -
Criteria applied: PM3_VSTR,PM5_STR,PP1_STR,PS3_MOD,PP3 -
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PM1, PM3, PM5, PP2, PP3, PP5 -
Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with Stargardt disease (MIM#248200) and other eye conditions (OMIM). (I) 0106 - This gene is associated with autosomal recessive disease (OMIM). (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 glycine to glutamic acid. (I) 0252 - This variant is homozygous. (I) 0305 - Variant is present in gnomAD >=0.01 and <0.03 for a recessive condition (v2: 1271 heterozygotes, 10 homozygotes). (I) 0309 - An alternative amino acid change at the same position has been observed in gnomAD (v2) (26 heterozygotes, 0 homozygotes). (I) 0502 - Missense variant with conflicting in silico predictions and high conservation. (I) 0600 - Variant is located in the annotated NBD2 domain (PMID: 29847635). (I) 0701 - Other missense variants comparable to the one identified in this case have very strong previous evidence for pathogenicity. p.(Gly1961Ala) has been previously reported in patients with Stargardt disease (ClinVar, PMID: 22427542). (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals with mild and later onset Stargardt disease (ClinVar, PMID: 22661473, PMID: 28327576, PMID: 28130426, PMID: 29925512). (SP) 1002 - This variant has moderate functional evidence supporting abnormal protein function, where transfected cells displayed reduced ATPase activity and substrate binding (PMID: 29847635). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -
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identified in compound heterozygous state in affected individual/s with macular isease -
The c.5882G>A (p.Gly1961Glu) missense variant in the ABCA4 gene has been previously reported in multiple individuals affected with Stargardt Disease (Kousal et al., 2014; Fritsche et al., 2012; Burke et al., 2012; Cella et al., 2009). This variant was observed at a significantly higher frequency in affected individuals than in a control population (OR=41.03 (5.4-310.1)). Furthermore, this variant is predicted to lie within a nucleotide binding domain, and in vitro functional assays demonstrated that this variant resulted in decreased ATP-binding capacity and ATP hydrolysis, despite an increase of the total amount of ABCA4 protein (Sun et al., 2000). Multiple in silico algorithms predict this variant to have a deleterious effect (GERP=5.35; CADD = 23.6; PolyPhen = 1.0; SIFT = 0.0). Emory Genetics Laboratory has classified this variant as Pathogenic. Therefore, this collective evidence supports the classification of the c.5882G>A (p.Gly1961Glu) as a Pathogenic variant for Stargardt Disease. We have confirmed this finding in our laboratory using Sanger sequencing. -
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GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. -
The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.020%). Predicted Consequence/Location: Missense variant Functional studies provide strong evidence of the variant having a damaging effect on the gene or gene product (PMID: 31599023). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.94; 3Cnet: 0.98). Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000043566 /PMID: 12676893 /3billion dataset). The variant has been reported to be in trans with a pathogenic variant as either compound heterozygous or homozygous in at least 2 similarly affected unrelated individuals (PMID: 12676893, 23504402, 30303587). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline. -
This variant c.5882G>A (p.Gly1961Glu) in ABCA4 gene has been observed in many individuals with autosomal recessive Stargardt disease, and has been found in trans (on the opposite chromosome) from many different pathogenic variants (PMID: Stone et al., 2017; Riera et al., 2017). This variant is present in population databases (rs1800553, ExAC 1.5%), including several homozygous individuals, and has an allele count higher than expected for a pathogenic variant (Kobayashi et al., 2017). However, this variant appears to be significantly enriched in individuals with Stargardt compared to the general population (Lee et al., 2017). This variant appears to be associated with milder and/or later onset disease (Lee et al., 2017). This variant has been reported to affect ABCA4 protein function (Sun et al. 2000). The amino acid Gly at position 1961 is changed to a Glu changing protein sequence and it might alter its composition and physico-chemical properties. The variant is predicted to be damaging by SIFT and the residue is conserved across species. The amino acid change p.Gly1961Glu in ABCA4 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Pathogenic. -
not provided Pathogenic:9Other:2
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The ABCA4 c.5882G>A; p.Gly1961Glu variant (rs1800553) has been reported in the medical literature in both the homozygous and compound heterozygous state in many individuals with ABCA4-related diseases (Allikmets 1997, Cella 2009, Garces 2018, Salles 2017, Wiszniewski 2005). Studies on individuals homozygous for this variant indicate that it is most often associated with milder, later onset retinal disease (Burke 2012). The variant is described as pathogenic or likely pathogenic by several sources in the ClinVar database (Variation ID: 7888). The variant is also described as one of the most common pathogenic variant in Stargardt patients (Burke 2012) and is found in the general population with an overall allele frequency of 0.5% (1291/282848 alleles, including 10 homozygotes) and an allele frequency of 1.4% (422/30614 alleles) in the South Asian population in the Genome Aggregation Database. The glycine at this position is highly conserved and computational algorithms predict this variant is deleterious. In support of this prediction, functional studies show this variant lies in a critical functional domain and results in reduced function of this variant protein compared to the wild type protein (Garces 2018, Sun 2000). Considering available information, this variant is classified as pathogenic but may result in a milder clinical phenotype. References: Allikmets R et al. Mutation of the Stargardt disease gene (ABCR) in age-related macular degeneration. Science. 1997 Sep 19;277(5333):1805-7. Burke TR et al. Retinal phenotypes in patients homozygous for the G1961E mutation in the ABCA4 gene. Invest Ophthalmol Vis Sci. 2012 Jul 3;53(8):4458-67. Cella W et al. G1961E mutant allele in the Stargardt disease gene ABCA4 causes bull's eye maculopathy. Exp Eye Res. 2009 Jun 15;89(1):16-24 Garces F et al. Correlating the Expression and Functional Activity of ABCA4 Disease Variants With the Phenotype of Patients With Stargardt Disease. Invest Ophthalmol Vis Sci. 2018 May 1;59(6):2305-2315. Salles MV et al. Novel Complex ABCA4 Alleles in Brazilian Patients With Stargardt Disease: Genotype-Phenotype Correlation. Invest Ophthalmol Vis Sci. 2017 Nov 1;58(13):5723-5730 Sun H et al. Biochemical defects in ABCR protein variants associated with human retinopathies. Nat Genet. 2000 Oct;26(2):242-6. 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 -
ABCA4: PM3:Very Strong, PP1:Strong, PM5, PM2:Supporting, PP3, PS3:Supporting -
The ABCA4 p.Gly1961Glu variant was identified in the literature in several homozygous or compound heterozygous individuals with ABCA4-related conditions (Stargardt disease 1, autosomal recessive retinitis pigmentosa, cone-rod dystrophy); this variant is typically associated with a milder phenotype and late-onset disease (Cella_2009_PMID:19217903; Burke_2012_PMID:22661473; Wiszniewski_2005_PMID:16103129; Kaway_2017_PMID:28611652; Zernant_2018_PMID:29848554). Furthermore, this variant is also seen to segregate with autosomal recessive retinitis pigmentosa, as seen in a large consanguineous family where this variant was identified in three affected compound heterozygotes (Ducroq_2006_PMID:16896346). The variant was identified in dbSNP (ID: rs1800553) and ClinVar (classified as pathogenic by Laboratory for Molecular Medicine, GeneDx and ten other laboratories, and as likely pathogenic by Mendelics and four other laboratories). The variant was identified in control databases in 1291 of 282848 chromosomes (10 homozygous) at a frequency of 0.004564 (Genome Aggregation Database March 6, 2019, v2.1.1). The variant was observed in the following populations: Ashkenazi Jewish in 242 of 10368 chromosomes (freq: 0.02334), South Asian in 422 of 30614 chromosomes (freq: 0.01378), Other in 41 of 7222 chromosomes (freq: 0.005677), European (non-Finnish) in 488 of 129158 chromosomes (freq: 0.003778), Latino in 68 of 35440 chromosomes (freq: 0.001919), European (Finnish) in 15 of 25124 chromosomes (freq: 0.000597), African in 10 of 24970 chromosomes (freq: 0.000401), and East Asian in 5 of 19952 chromosomes (freq: 0.000251). 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. The p.Gly1961 residue is conserved across mammals and other organisms, and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) suggest that the variant may impact the protein. Further, functional analysis has demonstrated that this variant results in reduced basal and retinal-stimulated ATPase activities compared to control (Sun_2000_PMID:11017087). In summary, based on the above information this variant meets our laboratory’s criteria to be classified as pathogenic. -
This sequence change replaces glycine, which is neutral and non-polar, with glutamic acid, which is acidic and polar, at codon 1961 of the ABCA4 protein (p.Gly1961Glu). This variant is present in population databases (rs1800553, gnomAD 2.3%), including at least one homozygous and/or hemizygous individual. This variant has been observed in many individuals with autosomal recessive Stargardt disease, and has been found in trans (on the opposite chromosome) from many different pathogenic variants (PMID: 28559085, 28181551, 30060493, 19074458, 29555955). This variant appears to be significantly enriched in individuals with Stargardt compared to the general population (PMID: 28327576). In addition, in a large meta-analysis, this variant conferred a 3.2-fold increased risk (95% CI: 1.74–5.95) for age-related macular degeneration in heterozygous carriers (PMID: 25921964). This variant appears to be associated with milder and/or later onset disease (PMID: 28327576, 28446513). ClinVar contains an entry for this variant (Variation ID: 7888). 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%. Experimental studies have shown that this missense change affects ABCA4 function (PMID: 11017087, 29847635). In summary, this variant is reported to cause disease. However, because this variant is associated with a milder form of disease than other pathogenic alleles in the ABCA4 gene, and because it is found in homozygosity in healthy individuals, it has been classified as Pathogenic (low penetrance). -
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Published functional studies demonstrate this variant results in reduced ATPase activity (Sun et al., 2000); Reported as pathogenic in ClinVar by different clinical laboratories but additional evidence is not available (ClinVar Variation ID: 7888; ClinVar); 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: 25921964, 25082885, 26593885, 28611652, 9295268, 22661473, 31980526, 32581362, 31589614, 32000842, 32619608, 33090715, 32783370, 32815999, 33301772, 32037395, 10958763, 15614537, 21786275, 16103129, 22025579, 22264887, 24265693, 25097241, 25087612, 11017087, 19217903, 25640233, 27775217, 27884173, 27535533, 26247787, 27414126, 28327576, 28044389, 29555955, 28130426, 29847635, 28224992, 30060493, 28181551, 29114839, 28492530, 28118664, 29769798, 28157192, 30609409, 30924848, 29925512, 30718709, 29765157, 28559085, 30156925, 18161617, 31814694, 32141364, 31456290, 32036094, 32845068, 34327195, 34426522, 33909047, 34008892, 33302505, 31573552) -
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Cone-rod dystrophy 3 Pathogenic:4
This ABCA4 variant (rs1800553) is among the most frequent retinal dystrophy-associated variants with an allele frequency of ~1.4% in South Asians. It has an entry in ClinVar. Individuals homozygous for p.Gly1961Glu show a range of retinal abnormalities but typically have a milder clinical presentation than individuals with additional ABCA4 variants on the opposite chromosome. This variant is located within a nucleotide binding domain of ABCA4, and functional studies demonstrate that this variant results in reduced ATPase activity9,10. This variant alone is not expected to cause CORD3. We consider c.5882G>A to be pathogenic. -
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Retinal dystrophy Pathogenic:4
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Stargardt disease Pathogenic:4
The p.Gly1961Glu (NM_000350.2 c.5882G>A) variant in ABCA4 has been reported >20 individuals with Stargardt disease and other retinal phenotypes and segregated with disease in 5 affected individuals from 5 families, but has been associated with reduced penetrance (Allikmets 1997 PMID:9295268, Burke 2012 PMID:22312191, Burke 2012 PMID:22661473, Song 2011 PMID:22025579, Burke 2010 PMID:20696155, Wiszniewski 2005 PMID:16103129, Cella 2009 PMID:19217903, Cideciyan 2009 PMID: 19074458). The variant shows a statistically significant (p<0.0001) difference in allele frequency in cases (5%) compared to the general population (0.4%, http://gnomad.broadinstitute.org). In vitro functional studies support an impact on protein function (Sun 2000 PMID:11017087). This variant has also been reported as Pathogenic by multiple clinical labs in ClinVar (Variation ID 7879). In summary, this variant meets criteria to be classified as pathogenic for Stargardt disease in an autosomal recessive manner, though it may show reduced penetrance and a milder clinical presentation compared to other pathogenic variants in the ABCA4 gene. ACMG/AMP Criteria applied: PS3_Supporting, PM3_VeryStrong, PP1_Strong. -
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Age related macular degeneration 2 Pathogenic:3
This variant was classified as: Likely pathogenic. The following ACMG criteria were applied in classifying this variant: Pm1,PM5,PP3,PP5. -
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Macular dystrophy Pathogenic:3
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This variant was identified aspotentially compound heterozygous with NM_000350.3:c.3113C>T and NM_000350.3:c.1622T>C. Criteria applied: PM3_VSTR, PS3_SUP, PM5_STR, PP3 -
Retinitis pigmentosa 19 Pathogenic:3
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The observed missense c.5882G>A(p.Gly1961Glu) variant in ABCA4 gene has been observed in homozygous, heterozygous and compound heterozygous states in multiple individuals affected with ABCA4-related retinal disorders (Birtel J, et al., 2018; Stone EM, et al., 2017; Burke TR, et al., 2012). This variant has been reported to segregate with disease in affected individuals (Cideciyan AV, et al., 2009). Functional studies indicate that the p.Gly1961Glu variant results in reduced ATPase activity and ATP binding, therefore, affecting ABCA4 protein function (Garces F, et al., 2018; Burke TR, et al., 2012). The p.Gly1961Glu variant has been reported with allele frequency of 0.5% in gnomAD Exomes. This variant has been submitted to the ClinVar database as Benign / Uncertain significance / Likely Pathogenic / Risk factor / Pathogenic (multiple submissions). The amino acid change p.Gly1961Glu in ABCA4 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. The amino acid Gly at position 1961 is changed to a Glu changing protein sequence and it might alter its composition and physico-chemical properties. Multiple lines of computational evidences (Polyphen - Probably damaging , SIFT - Damaging and MutationTaster - Disease causing) predict a damaging effect on protein structure and function for this variant. This variant, being one of the most common ABCA4 variant, has been highly associated with Stargardt disease (Lewis RA, et al., 1999) and has been shown to confer a a 3.2-fold increased risk for age-related macular degeneration (Zhang R, et al., 2015). This variant appears to be associated with milder phenotype of retinal disorders, suggesting that this variant shows low penetrance (Zernant J, et al., 2017). For these reasons, this variant has been classified as Pathogenic (risk factor - low penetrance). The same variant in ABCA4 gene has been identified in heterozygous state in spouse. -
Criteria applied: PM3_VSTR,PM5_STR,PP1_STR,PS3_MOD,PP3,PP4 -
ABCA4-related disorder Pathogenic:3
The ABCA4 c.5882G>A (p.Gly1961Glu) missense variant has been reported in at least eight studies in which it is found in over 50 individuals, 54 of whom were diagnosed with Stargardt disease, including 18 who carry the variant in a homozygous state, in at least 26 who carry the variant in a compound heterozygous state, and in seven who carry the variant in a heterozygous state. The p.Gly1961Glu variant is also found in a heterozygous state in two asymptomatic individuals (Allikmets et al. 1997; Wiszniewski et al. 2005; Kitiratschky et al. 2008; Cella et al. 2009; Burke et al. 2012; Burke et al. 2012; Fujinami et al. 2013; Lee et al. 2016). The p.Gly1961Glu variant is associated with a mild phenotype. Fifteen of the individuals carrying the variant exhibited bull's eye maculopathy and retinal dysfunction limited to the macula and not typical general dysfunction (Cella et al. 2009). Six individuals were found to carry additional variants in the ABCA4 gene and exhibited a more severe phenotype (Burke et al. 2012). The p.Gly1961Glu variant was absent from 220 control individuals and is reported at a frequency of 0.01498 in the South Asian population of the Exome Aggregation Consortium. Haplotype analysis in the South Asian population suggested that the p.Gly1961Glu variant has a founder effect in this population (Fujinami et al. 2013). Functional studies demonstrated that the p.Gly1961Glu variant protein resulted in reduced ATPase activity and ATP binding, while maintaining expression levels comparable to wild type, which is consistent with a mild phenotype. Additionally, the variant protein ATPase activity was inhibited by all-trans retinal, in contrast to the stimulation seen in wild type (Sun et al. 2000; Burke et al 2012a). Based on the collective evidence, the p.Gly1961Glu 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 ABCA4 c.5882G>A variant is predicted to result in the amino acid substitution p.Gly1961Glu. This variant has been reported many times in the compound heterozygous state in individuals with retinal dystrophy and has been associated with later-onset and milder retinal phenotypes (see for examples Cella et al. 2009. PubMed ID: 19217903, Lewis et al. 1999. PubMed ID: 9973280, Allikmets et al. 1997. PubMed ID: 9295268, Fujinami et al. 2013. PubMed ID: 23769331). This variant is documented with a global allele frequency of 0.46% in gnomAD and with the highest allele frequency of 2.3% in individuals of Ashkenazi Jewish descent, including several homozygotes. This allele frequency is relatively high and consistent with this variant causing a more mild and later-onset retinal phenotype (Burke et al. 2012. PubMed ID: 22661473). However, when this variant is present in cis with other pathogenic ABCA4 variants as a complex allele, it has been reported to cause severe retinal phenotypes (Burke et al. 2012. PubMed ID: 22661473). Given the evidence, we interpret c.5882G>A (p.Gly1961Glu), both alone and as part of a complex allele, as pathogenic. -
This is a nonsynonymous variant in the ABCA4 gene (OMIM 601691). Biallelic pathogenic variants in this gene have been associated with autosomal recessive ABCA4-related disorders. This variant has been reported in the homozygous or compound heterozygous state in many individuals with mild or late-onset ABCA4-related disease (PMID: 30060493, 29555955, 28559085, 19074458, 28181551) (PM3_Strong). Additionally, this variant has been shown to confer a moderate risk (~3-fold) for age-related macular degeneration (PMID: 25921964). Functional studies have shown that this variant alters ABCA4 protein function (PMID: 11017087, 29847635) (PS3). An alternate amino acid change at this position (p.Gly1961Arg) has been previously reported as pathogenic in affected individuals (PMID: 23755871, 19074458, 26780318, 28118664) (PM5). Multiple computational algorithms predict a deleterious effect for this amino acid substitution (PP3). This variant has a 1.378% maximum allele frequency in non-founder control populations (https://gnomad.broadinstitute.org/). Based on current evidence, this variant is classified as pathogenic for autosomal recessive ABCA4-related disorders. -
Inborn genetic diseases Pathogenic:1
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ABCA4-related retinopathy Pathogenic:1
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Retinitis pigmentosa Pathogenic:1
The p.Gly1961Glu 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: PS3, PM5, PP3, PP5. 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. -
Severe early-childhood-onset retinal dystrophy;C1858806:Cone-rod dystrophy 3;C1866422:Retinitis pigmentosa 19 Pathogenic:1
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See cases Pathogenic:1
ACMG categories: PS3,PM1,PM3,PP3,PP4 -
Severe early-childhood-onset retinal dystrophy;C1858806:Cone-rod dystrophy 3;C1866422:Retinitis pigmentosa 19;C3495438:Age related macular degeneration 2 Pathogenic:1
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not specified Benign:1
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MACULAR DEGENERATION, AGE-RELATED, 2, SUSCEPTIBILITY TO Other:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at