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

Genomes: 𝑓 0.0031 ( 3 hom., cov: 32)
Exomes 𝑓: 0.0034 ( 41 hom. )

Consequence

ABCA4
NM_000350.3 missense

Scores

8
7
3

Clinical Significance

Pathogenic/Likely pathogenic/Pathogenic, low penetrance criteria provided, multiple submitters, no conflicts P:58B:1O:4

Conservation

PhyloP100: 5.88
Variant links:
Genes affected
ABCA4 (HGNC:34): (ATP binding cassette subfamily A member 4) The membrane-associated protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intracellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White). This protein is a member of the ABC1 subfamily. Members of the ABC1 subfamily comprise the only major ABC subfamily found exclusively in multicellular eukaryotes. This protein is a retina-specific ABC transporter with N-retinylidene-PE as a substrate. It is expressed exclusively in retina photoreceptor cells, and the gene product mediates transport of an essental molecule, all-trans-retinal aldehyde (atRAL), across the photoreceptor cell membrane. Mutations in this gene are found in patients diagnosed with Stargardt disease, a form of juvenile-onset macular degeneration. Mutations in this gene are also associated with retinitis pigmentosa-19, cone-rod dystrophy type 3, early-onset severe retinal dystrophy, fundus flavimaculatus, and macular degeneration age-related 2. [provided by RefSeq, Sep 2019]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 10 ACMG points.

PM1
In a hotspot region, there are 4 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 1 benign, 5 uncertain in NM_000350.3
PM5
Other missense variant is known to change same aminoacid residue: Variant chr1-94008252-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 236140.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
PP5
Variant 1-94008251-C-T is Pathogenic according to our data. Variant chr1-94008251-C-T is described in ClinVar as [Pathogenic_low_penetrance]. Clinvar id is 7888.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. We mark this variant Likely_pathogenic, oryginal submissions are: {Pathogenic_low_penetrance=1, Benign=1, Pathogenic=32, Likely_pathogenic=11, not_provided=3}. Variant chr1-94008251-C-T is described in Lovd as [Likely_pathogenic]. Variant chr1-94008251-C-T is described in Lovd as [Pathogenic]. Variant chr1-94008251-C-T is described in Lovd as [Likely_benign]. Variant chr1-94008251-C-T is described in Lovd as [Likely_pathogenic]. Variant chr1-94008251-C-T is described in Lovd as [Pathogenic]. Variant chr1-94008251-C-T is described in Lovd as [Pathogenic].
BP4
Computational evidence support a benign effect (MetaRNN=0.013598174). . Strength limited to SUPPORTING due to the PP5.
BS1
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00311 (473/152210) while in subpopulation SAS AF= 0.0127 (61/4814). AF 95% confidence interval is 0.0101. There are 3 homozygotes in gnomad4. There are 239 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ABCA4NM_000350.3 linkc.5882G>A p.Gly1961Glu missense_variant Exon 42 of 50 ENST00000370225.4 NP_000341.2 P78363Q6AI28
ABCA4NM_001425324.1 linkc.5660G>A p.Gly1887Glu missense_variant Exon 41 of 49 NP_001412253.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ABCA4ENST00000370225.4 linkc.5882G>A p.Gly1961Glu missense_variant Exon 42 of 50 1 NM_000350.3 ENSP00000359245.3 P78363
ABCA4ENST00000465352.1 linkn.298G>A non_coding_transcript_exon_variant Exon 3 of 6 5

Frequencies

GnomAD3 genomes
AF:
0.00311
AC:
473
AN:
152092
Hom.:
3
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000555
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00380
Gnomad ASJ
AF:
0.0239
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.0127
Gnomad FIN
AF:
0.000943
Gnomad MID
AF:
0.0222
Gnomad NFE
AF:
0.00325
Gnomad OTH
AF:
0.00478
GnomAD3 exomes
AF:
0.00470
AC:
1181
AN:
251452
Hom.:
9
AF XY:
0.00537
AC XY:
730
AN XY:
135906
show subpopulations
Gnomad AFR exome
AF:
0.000492
Gnomad AMR exome
AF:
0.00188
Gnomad ASJ exome
AF:
0.0237
Gnomad EAS exome
AF:
0.000272
Gnomad SAS exome
AF:
0.0138
Gnomad FIN exome
AF:
0.000508
Gnomad NFE exome
AF:
0.00348
Gnomad OTH exome
AF:
0.00570
GnomAD4 exome
AF:
0.00344
AC:
5025
AN:
1461802
Hom.:
41
Cov.:
31
AF XY:
0.00384
AC XY:
2792
AN XY:
727210
show subpopulations
Gnomad4 AFR exome
AF:
0.00108
Gnomad4 AMR exome
AF:
0.00177
Gnomad4 ASJ exome
AF:
0.0222
Gnomad4 EAS exome
AF:
0.000529
Gnomad4 SAS exome
AF:
0.0131
Gnomad4 FIN exome
AF:
0.00122
Gnomad4 NFE exome
AF:
0.00239
Gnomad4 OTH exome
AF:
0.00546
GnomAD4 genome
AF:
0.00311
AC:
473
AN:
152210
Hom.:
3
Cov.:
32
AF XY:
0.00321
AC XY:
239
AN XY:
74422
show subpopulations
Gnomad4 AFR
AF:
0.000554
Gnomad4 AMR
AF:
0.00379
Gnomad4 ASJ
AF:
0.0239
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.0127
Gnomad4 FIN
AF:
0.000943
Gnomad4 NFE
AF:
0.00325
Gnomad4 OTH
AF:
0.00473
Alfa
AF:
0.00457
Hom.:
6
Bravo
AF:
0.00284
TwinsUK
AF:
0.000809
AC:
3
ALSPAC
AF:
0.00208
AC:
8
ESP6500AA
AF:
0.00113
AC:
5
ESP6500EA
AF:
0.00419
AC:
36
ExAC
AF:
0.00505
AC:
613
Asia WGS
AF:
0.00520
AC:
18
AN:
3478
EpiCase
AF:
0.00480
EpiControl
AF:
0.00451

ClinVar

Significance: Pathogenic/Likely pathogenic/Pathogenic, low penetrance
Submissions summary: Pathogenic:58Benign:1Other:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Severe early-childhood-onset retinal dystrophy Pathogenic:19Other:1
May 28, 2019
Mendelics
Significance: Likely pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Jul 01, 2008
OMIM
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: literature only

- -

Jul 26, 2022
MGZ Medical Genetics Center
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Jan 17, 2020
Baylor Genetics
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868]. -

-
Neuberg Centre For Genomic Medicine, NCGM
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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. -

Dec 30, 2017
Department Of Genetics, Sultan Qaboos University Hospital, Sultan Qaboos University
Significance: Likely pathogenic
Review Status: criteria provided, single submitter
Collection Method: curation

- -

Sep 10, 2021
Genome-Nilou Lab
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Jun 28, 2016
Knight Diagnostic Laboratories, Oregon Health and Sciences University
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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. -

Mar 25, 2024
Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre
Significance: Likely pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Jan 01, 2016
Institute of Human Genetics, Univ. Regensburg, Univ. Regensburg
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Jan 03, 2022
3billion, Medical Genetics
Significance: Likely pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000007888, PMID:9295268, PS1_S). A different missense change at the same codon has been reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000236140, PMID:22427542,NULL, PM5_M). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.76, 3CNET: 0.857, PP3_P). A missense variant is a common mechanism associated with Stargardt disease 1 (PP2_P). Therefore, this variant is classified as likely pathogenic according to the recommendation of ACMG/AMP guideline. -

-
Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine
Significance: Likely pathogenic
Review Status: criteria provided, single submitter
Collection Method: research

identified in compound heterozygous state in affected individual/s with macular isease -

Oct 01, 2021
Laboratory of Medical Genetics, National & Kapodistrian University of Athens
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

PM1, PM3, PM5, PP2, PP3, PP5 -

Feb 05, 2025
SingHealth Duke-NUS Institute of Precision Medicine
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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) -

Sep 02, 2022
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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 -

Jan 30, 2021
Institute of Medical Molecular Genetics, University of Zurich
Significance: Likely pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

May 29, 2024
Institute of Human Genetics, University of Leipzig Medical Center
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

Criteria applied: PM3_VSTR,PM5_STR,PP1_STR,PS3_MOD,PP3 -

-
GenomeConnect, ClinGen
Significance: not provided
Review Status: no classification provided
Collection Method: phenotyping only

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. -

Feb 01, 2013
Arcensus
Significance: Likely pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

-
Juno Genomics, Hangzhou Juno Genomics, Inc
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

PM3_VeryStrong+PP4+PM2_Supporting+PM5+PP3 -

not provided Pathogenic:9Other:2
-
Clinical Genetics, Academic Medical Center
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: clinical testing

- -

-
NEI Ophthalmic Genomics Laboratory, National Institutes of Health
Significance: not provided
Review Status: no classification provided
Collection Method: literature only

- -

Apr 12, 2022
GeneDx
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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) -

Jul 01, 2024
CeGaT Center for Human Genetics Tuebingen
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

ABCA4: PM3:Very Strong, PP1:Strong, PM5, PM2:Supporting, PP3, PS3:Supporting -

Nov 30, 2016
Eurofins Ntd Llc (ga)
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

-
Retina International
Significance: not provided
Review Status: no classification provided
Collection Method: literature only

- -

Feb 02, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Pathogenic, low penetrance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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). -

-
Department of Pathology and Laboratory Medicine, Sinai Health System
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: clinical testing

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. -

-
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: clinical testing

- -

-
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: clinical testing

- -

Oct 21, 2022
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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 -

Cone-rod dystrophy 3 Pathogenic:4
Jul 01, 2008
OMIM
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: literature only

- -

Jan 01, 2019
Institute of Human Genetics, University of Leipzig Medical Center
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Apr 14, 2021
Johns Hopkins Genomics, Johns Hopkins University
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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. -

Jun 10, 2016
Division of Human Genetics, Children's Hospital of Philadelphia
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: research

- -

Retinal dystrophy Pathogenic:4
Jan 01, 2023
Institute of Human Genetics, Univ. Regensburg, Univ. Regensburg
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Jan 01, 2015
NIHR Bioresource Rare Diseases, University of Cambridge
Significance: Likely pathogenic
Review Status: no assertion criteria provided
Collection Method: research

- -

Aug 17, 2019
Blueprint Genetics
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Oct 01, 2023
Dept Of Ophthalmology, Nagoya University
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: research

- -

Stargardt disease Pathogenic:4
Apr 01, 2018
Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: research

- -

May 28, 2020
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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. -

Oct 25, 2021
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen
Significance: Likely pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Jun 23, 2019
Sharon lab, Hadassah-Hebrew University Medical Center
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: research

- -

Age related macular degeneration 2 Pathogenic:3
-
Genomics England Pilot Project, Genomics England
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Sep 01, 2016
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: clinical testing

- -

Sep 05, 2019
Centre for Mendelian Genomics, University Medical Centre Ljubljana
Significance: Likely pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This variant was classified as: Likely pathogenic. The following ACMG criteria were applied in classifying this variant: Pm1,PM5,PP3,PP5. -

Macular dystrophy Pathogenic:3
Jan 01, 2015
NIHR Bioresource Rare Diseases, University of Cambridge
Significance: Likely pathogenic
Review Status: no assertion criteria provided
Collection Method: research

- -

Nov 22, 2021
Institute of Human Genetics, University of Leipzig Medical Center
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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 -

Apr 01, 2018
Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet
Significance: Likely pathogenic
Review Status: no assertion criteria provided
Collection Method: research

- -

Retinitis pigmentosa 19 Pathogenic:3
-
Genomics England Pilot Project, Genomics England
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

May 20, 2023
Neuberg Centre For Genomic Medicine, NCGM
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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. -

Jun 19, 2024
Institute of Human Genetics, University of Leipzig Medical Center
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

Criteria applied: PM3_VSTR,PM5_STR,PP1_STR,PS3_MOD,PP3,PP4 -

ABCA4-related disorder Pathogenic:3
May 08, 2017
Illumina Laboratory Services, Illumina
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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. -

Aug 28, 2024
PreventionGenetics, part of Exact Sciences
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: clinical testing

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. -

Nov 04, 2022
Variantyx, Inc.
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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. -

ABCA4-related retinopathy Pathogenic:1
Aug 29, 2023
Intergen, Intergen Genetics and Rare Diseases Diagnosis Center
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Inborn genetic diseases Pathogenic:1
Sep 07, 2014
Ambry Genetics
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Retinitis pigmentosa Pathogenic:1
-
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard
Significance: Likely pathogenic
Review Status: criteria provided, single submitter
Collection Method: curation

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
Jun 20, 2019
Hadassah Hebrew University Medical Center
Significance: Likely pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

See cases Pathogenic:1
Mar 09, 2023
Institute of Human Genetics, University Hospital Muenster
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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
Mar 26, 2024
Fulgent Genetics, Fulgent Genetics
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

not specified Benign:1
Feb 11, 2020
Al Jalila Children’s Genomics Center, Al Jalila Childrens Speciality Hospital
Significance: Benign
Review Status: flagged submission
Collection Method: clinical testing

- -

MACULAR DEGENERATION, AGE-RELATED, 2, SUSCEPTIBILITY TO Other:1
Jul 01, 2008
OMIM
Significance: risk factor
Review Status: no assertion criteria provided
Collection Method: literature only

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.85
BayesDel_addAF
Uncertain
0.10
D
BayesDel_noAF
Pathogenic
0.39
CADD
Pathogenic
27
DANN
Uncertain
1.0
DEOGEN2
Uncertain
0.74
D;D
Eigen
Uncertain
0.35
Eigen_PC
Uncertain
0.45
FATHMM_MKL
Pathogenic
0.99
D
LIST_S2
Pathogenic
0.99
D;D
MetaRNN
Benign
0.014
T;T
MetaSVM
Uncertain
0.72
D
MutationAssessor
Benign
-0.12
.;N
PrimateAI
Pathogenic
0.81
D
PROVEAN
Pathogenic
-6.6
.;D
REVEL
Pathogenic
0.76
Sift
Uncertain
0.0010
.;D
Sift4G
Pathogenic
0.0010
D;D
Polyphen
1.0
.;D
Vest4
0.96
MVP
0.95
MPC
0.53
ClinPred
0.071
T
GERP RS
5.3
Varity_R
0.93
gMVP
0.95

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1800553; hg19: chr1-94473807; COSMIC: COSV64673416; COSMIC: COSV64673416; API