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NM_000350.3(ABCA4):c.5882G>A (p.Gly1961Glu) AND Severe early-childhood-onset retinal dystrophy

Germline classification:
Pathogenic/Likely pathogenic (18 submissions)
Last evaluated:
May 29, 2024
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000008340.41

Allele description [Variation Report for NM_000350.3(ABCA4):c.5882G>A (p.Gly1961Glu)]

NM_000350.3(ABCA4):c.5882G>A (p.Gly1961Glu)

Gene:
ABCA4:ATP binding cassette subfamily A member 4 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1p22.1
Genomic location:
Preferred name:
NM_000350.3(ABCA4):c.5882G>A (p.Gly1961Glu)
HGVS:
  • NC_000001.11:g.94008251C>T
  • NG_009073.1:g.117899G>A
  • NG_009073.2:g.117897G>A
  • NM_000350.3:c.5882G>AMANE SELECT
  • NM_001425324.1:c.5660G>A
  • NP_000341.2:p.Gly1961Glu
  • NP_000341.2:p.Gly1961Glu
  • NP_001412253.1:p.Gly1887Glu
  • NC_000001.10:g.94473807C>T
  • NM_000350.2:c.5882G>A
  • P78363:p.Gly1961Glu
Protein change:
G1887E; GLY1961GLU
Links:
UniProtKB: P78363#VAR_008475; OMIM: 601691.0007; dbSNP: rs1800553
NCBI 1000 Genomes Browser:
rs1800553
Molecular consequence:
  • NM_000350.3:c.5882G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001425324.1:c.5660G>A - missense variant - [Sequence Ontology: SO:0001583]
Observations:
6

Condition(s)

Name:
Severe early-childhood-onset retinal dystrophy (STGD1)
Synonyms:
MACULAR DYSTROPHY WITH FLECKS, TYPE 1; STGD; Stargardt macular dystrophy; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0009549; MeSH: D000080362; MedGen: C1855465; Orphanet: 827; OMIM: 248200

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000028548OMIM
no assertion criteria provided
Pathogenic
(Jul 1, 2008)
germlineliterature only

PubMed (4)
[See all records that cite these PMIDs]

SCV000267674Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine
criteria provided, single submitter

(Lee et al. (Hum Genet 2016))
Likely pathogenicgermlineresearch

PubMed (1)
[See all records that cite this PMID]

SCV000281939Institute of Human Genetics, Univ. Regensburg, Univ. Regensburg
criteria provided, single submitter

(Schulz et al. (Invest Ophthalmol Vis Sci. 2017))
Pathogenic
(Jan 1, 2016)
germlineclinical testing

PubMed (15)
[See all records that cite these PMIDs]

SCV000494247Knight Diagnostic Laboratories, Oregon Health and Sciences University - CSER-NextGen
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jun 28, 2016)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV000607275GenomeConnect, ClinGen
no classification provided
not providedunknownphenotyping only

SCV000891470Department Of Genetics, Sultan Qaboos University Hospital, Sultan Qaboos University
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Dec 30, 2017)
unknowncuration

PubMed (1)
[See all records that cite this PMID]

SCV001135328Mendelics
criteria provided, single submitter

(Mendelics Assertion Criteria 2017)
Likely pathogenic
(May 28, 2019)
unknownclinical testing

Citation Link,

SCV001521357Baylor Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jan 17, 2020)
unknownclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001548126Institute of Medical Molecular Genetics, University of Zurich
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Jan 30, 2021)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

SCV001976708Laboratory of Medical Genetics, National & Kapodistrian University of Athens
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Oct 1, 2021)
maternalclinical testing

PubMed (2)
[See all records that cite these PMIDs]

SCV0020587833billion
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Jan 3, 2022)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

PMID:9295268,

SCV002100408Genome-Nilou Lab
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Sep 10, 2021)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV002526676Institute of Human Genetics, University of Leipzig Medical Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(May 29, 2024)
unknownclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV002564625Arcensus
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Feb 1, 2013)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV002581171MGZ Medical Genetics Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jul 26, 2022)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV002767263Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Sep 2, 2022)
germlineclinical testing

PubMed (8)
[See all records that cite these PMIDs]

SCV004048390Neuberg Centre For Genomic Medicine, NCGM
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenicgermlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV004806246Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Mar 25, 2024)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes6not providednot provided336yesclinical testing, research
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing, phenotyping only
not providedgermlineno1not providednot providednot providedyesclinical testing, research
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedunknownyesnot providednot providednot providednot providednot providedclinical testing, curation
not providedmaternalyesnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

A photoreceptor cell-specific ATP-binding transporter gene (ABCR) is mutated in recessive Stargardt macular dystrophy.

Allikmets R, Singh N, Sun H, Shroyer NF, Hutchinson A, Chidambaram A, Gerrard B, Baird L, Stauffer D, Peiffer A, Rattner A, Smallwood P, Li Y, Anderson KL, Lewis RA, Nathans J, Leppert M, Dean M, Lupski JR.

Nat Genet. 1997 Mar;15(3):236-46. Erratum in: Nat Genet. 1997 Sep;17(1):122. doi: 10.1038/ng0997-122a.

PubMed [citation]
PMID:
9054934

Genotype/Phenotype analysis of a photoreceptor-specific ATP-binding cassette transporter gene, ABCR, in Stargardt disease.

Lewis RA, Shroyer NF, Singh N, Allikmets R, Hutchinson A, Li Y, Lupski JR, Leppert M, Dean M.

Am J Hum Genet. 1999 Feb;64(2):422-34.

PubMed [citation]
PMID:
9973280
PMCID:
PMC1377752
See all PubMed Citations (29)

Details of each submission

From OMIM, SCV000028548.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (4)

Description

In 6 of 167 patients with age-related macular dystrophy (ARMD2; 153800), Allikmets et al. (1997) found a gly1961-to-glu (G1961E) alteration in the ABCR gene. The associated pathology ranged from a few tiny juxtafoveal drusen in 1 eye of a patient (age 74 years), to confluent drusen and drusenoid retinal pigment epithelium (RPE) detachments (age 78 years), to various forms of soft to calcified macular drusen and extensive geographic atrophy (more than 1 disc diameter) (ages 81 and 82 years, respectively).

In a study of 150 families with recessive Stargardt disease (STGD1; 248200), Lewis et al. (1999) found that the G1961E mutation was present in 16 of 173 chromosomes in which mutation was identified. G1961E in heterozygous state had previously been associated with age-related macular degeneration. In 150 families with STGD1, a high frequency of ARMD in first- and second-degree relatives was found, suggesting that heterozygosity enhances susceptibility to ARMD.

In a 14-year-old female with cone dystrophy (CORD3; 604116), Kitiratschky et al. (2008) identified compound heterozygosity for a 5882G-A transition in exon 42 of the ABCA4 gene, resulting in the G1961E substitution, and a splice site mutation (601691.0030). The patient, who had onset of disease at 6 years of age, had a red-green defect of color vision, normal glare sensitivity and night vision, RPE atrophy of the macula and peripheral retina, central scotoma, and a reduced cone but normal rod electroretinogram (ERG). Both mutations were also identified in her affected brother, and their unaffected parents were each heterozygous for 1 of the mutations, respectively.

Lek et al. (2016) questioned the pathogenicity of this variant because the ExAC database lists 4 homozygotes with the variant as well as a high allele frequency (0.015) of the variant in the South Asian population.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine, SCV000267674.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided2not providedyesresearch PubMed (1)
2not provided1not providedyesresearch PubMed (1)

Description

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

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided2not providednot providednot provided
2germlinenonot providednot providednot provided1not providednot providednot provided

From Institute of Human Genetics, Univ. Regensburg, Univ. Regensburg, SCV000281939.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided48not providednot providedclinical testing PubMed (15)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyes335not providednot provided48not providednot providednot provided

From Knight Diagnostic Laboratories, Oregon Health and Sciences University - CSER-NextGen, SCV000494247.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenonot providednot providednot providednot providednot providednot providednot provided

From GenomeConnect, ClinGen, SCV000607275.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedphenotyping onlynot provided

Description

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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providedvalidationnot providednot providednot providednot provided

From Department Of Genetics, Sultan Qaboos University Hospital, Sultan Qaboos University, SCV000891470.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcuration PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot providednot providednot providednot providednot provided

From Mendelics, SCV001135328.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Baylor Genetics, SCV001521357.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

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

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot providednot providednot providednot providednot provided

From Institute of Medical Molecular Genetics, University of Zurich, SCV001548126.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Laboratory of Medical Genetics, National & Kapodistrian University of Athens, SCV001976708.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

PM1, PM3, PM5, PP2, PP3, PP5

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1maternalyesnot providednot providednot providednot providednot providednot providednot provided

From 3billion, SCV002058783.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)

Description

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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyes1not providednot provided1not providednot providednot provided

From Genome-Nilou Lab, SCV002100408.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Institute of Human Genetics, University of Leipzig Medical Center, SCV002526676.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

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

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot providednot providednot providednot providednot provided

From Arcensus, SCV002564625.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From MGZ Medical Genetics Center, SCV002581171.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided5not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided5not providednot providednot provided

From Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV002767263.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (8)

Description

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

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Neuberg Centre For Genomic Medicine, NCGM, SCV004048390.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, SCV004806246.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 24, 2024