Thirty-Three Truncated and 98 Amino Acid–Changing Variants in the ABCA4 Gene
This variant was found on one allele of a Stargardt patient, but no additional details are provided about the patient or the other allele. A combination of single-strand conformation polymorphism (SSCP) and automated DNA sequencing was used to evaluate the entire exonic and flanking intron sequence of the ABCA4 gene
413; 19c.1804C>T; c.2828G>Ap.R602W (D); p.R943Q (U)16c.2453G>Ap.G818E (D)Compound heterozygous
Case#: Sporadic Case #4, Mexican
DiseaseAssertion: Stargardt
FamilyInfo: n/a
CasePresentingHPOs:
CaseHPOFreeText: STGD diagnosis based on: "onset of symptoms in childhood or early adulthood (before 20 years of age), bilateral central vision loss (central and peripheral visual field computerized testing), a retinal “beaten-bronze” foveal appearance and/or yellow-whitish flecks from the posterior pole to the mid periphery, normal caliber of the retinal vessels, no pigmented bone spicules in the retinal periphery, a normal to subnormal electroretinogram, and a typical dark choroid in fluorescein angiography."
CaseNotHPOs:
CaseNotHPOFreeText:
PreviouslyPublished: n/a
Variant: allele 1: c.1804C>T (p.R602W) and c.2828G>A (p.R943Q) allele 2: c.2453G>A (p. G818E); direct sequencing of exons of ABCA4
ClinVar: 99135
CAID: CA227000
SupplementalData: n/a
816c.2453G>Ap.G818E (D)28c.4249_4251 delTTCp.F1417del (D; N)Compound heterozygous
Case#: Familial Case #8, Mexican
DiseaseAssertion: Stargardt
FamilyInfo: n/a
CasePresentingHPOs:
CaseHPOFreeText: STGD diagnosis based on: "onset of symptoms in childhood or early adulthood (before 20 years of age), bilateral central vision loss (central and peripheral visual field computerized testing), a retinal “beaten-bronze” foveal appearance and/or yellow-whitish flecks from the posterior pole to the mid periphery, normal caliber of the retinal vessels, no pigmented bone spicules in the retinal periphery, a normal to subnormal electroretinogram, and a typical dark choroid in fluorescein angiography."
CaseNotHPOs:
CaseNotHPOFreeText:
PreviouslyPublished: n/a
Variant: allele 1: c.2453G>A (p. G818E) allele 2: c.4249_4251 delTTC (p.F1417del); direct sequencing of exons of ABCA4
ClinVar: 99135
CAID: CA227000
SupplementalData: n/a
(P5: G818E/L541P+A1038V
This variant is mentioned for patient 5 but is likely the same proband as in PMID: 19074458 since this is the same first author and same genotype
Flow of individuals. A schematic representation showing the outcome of the 677 individuals with IRD participating in the study. *Supplementary Table 4. Indiv: individuals.
Case#: Patient #330
DiseaseAssertion: Stargardt
FamilyInfo: n/a
CasePresentingHPOs:
CaseHPOFreeText: "Patients clinically suspected of having a retinal dystrophy were selected for the targeted analysis based on evaluation of available clinical records (clinical diagnosis, clinical history, fundus changes, OCT imaging, ERG, visual acuity, visual fields, family history)."
CaseNotHPOs:
CaseNotHPOFreeText:
GenotypingMethod: NGS panel of 125 genes known to be associated with: retinitis pigmentosa, Bardet-Biedl syndrome, cone-rod dystrophy, Leber congenital amaurosis, Usher syndrome and congenital stationary night blindness (some genes cause more than one eye disorder).
PreviouslyPublished: n/a
Variant: 2453G>A (p.Gly818Glu)
ClinVar: 99135
CAID: CA227000
SupplementalData: supplemental table s4
1016c.2453G>Ap.G818E (D)16c.2453G>Ap.G818E (D)Homozygous
Case#: Sporadic Case #10, Mexican
DiseaseAssertion: Stargardt
FamilyInfo: n/a
CasePresentingHPOs:
CaseHPOFreeText: STGD diagnosis based on: "onset of symptoms in childhood or early adulthood (before 20 years of age), bilateral central vision loss (central and peripheral visual field computerized testing), a retinal “beaten-bronze” foveal appearance and/or yellow-whitish flecks from the posterior pole to the mid periphery, normal caliber of the retinal vessels, no pigmented bone spicules in the retinal periphery, a normal to subnormal electroretinogram, and a typical dark choroid in fluorescein angiography."
CaseNotHPOs:
CaseNotHPOFreeText:
PreviouslyPublished: n/a
Variant: c.2453G>A (p. G818E) homozygous; direct sequencing of exons of ABCA4
ClinVar: 99135
CAID: CA227000
SupplementalData: n/a
1545c.6221G>Tp.G2074V (D; N)16c.2453G>Ap.G818E (D)Compound heterozygous
Case#: Sporadic Case #15, Mexican
DiseaseAssertion: Stargardt
FamilyInfo: n/a
CasePresentingHPOs:
CaseHPOFreeText: STGD diagnosis based on: "onset of symptoms in childhood or early adulthood (before 20 years of age), bilateral central vision loss (central and peripheral visual field computerized testing), a retinal “beaten-bronze” foveal appearance and/or yellow-whitish flecks from the posterior pole to the mid periphery, normal caliber of the retinal vessels, no pigmented bone spicules in the retinal periphery, a normal to subnormal electroretinogram, and a typical dark choroid in fluorescein angiography."
CaseNotHPOs:
CaseNotHPOFreeText:
PreviouslyPublished: n/a
Variant: allele 1: c.6221G>T (p.G2074V) allele 2: c.2453G>A (p. G818E); direct sequencing of exons of ABCA4
ClinVar: 99135
CAID: CA227000
SupplementalData: n/a
Sixty-six individuals representing 54 families were studied (Supplementary Material, Table S1). All individuals were found to harbor two ABCA4 variants likely to cause the retinal disease (18,20–26). In 40 families (74%), independent segregation of the two alleles was demonstrated. The ages at the time of their first visit ranged from 9 to 74 years (mean = 35.9, median = 35.2 years); in the majority of individuals (36/66=55%), data were available from a second visit that occurred on average 8.7 years (range=2–20 years, median = 6.9 years) after the first visit.
Case#: Patient #35, male, 35yo at report, 14yo at onset,
DiseaseAssertion: STGD
FamilyInfo: family 30, segregation was noted as "yes" but no other details provided
CasePresentingHPOs:
CaseHPOFreeText:
CaseNotHPOs:
CaseNotHPOFreeText:
GenotypingMethod:
PreviouslyPublished: n/a
Variant: allele 1: A1038V;L541P allele 2: G818E
ClinVar: 99135
CAID: CA227000
SupplementalData: supplemental table 1
The locations of ABCA4 homozygous and hypomorphic missense mutations characterized in the present study are shown in Fig 1. These mutations are distributed throughout ABCA4 with 4 in ECD1 (p.Asn96Asp, p.Asn96His, p.Arg212Cys, p.Arg602Trp), 4 in ECD2 (p.Leu1430Pro, p.Gly1439Asp, p.Pro1486Leu, p.Ala1598Asp), 6 within or close to NBD1 (p.Gly863Ala, p.Asn965Ser, p.Thr1019Met, p.Glu1087Lys, p.Arg1108Cys, p.Arg1129Leu), and 6 within NBD2 (p.Leu1940Pro, p.Gly1977Ser, p.Leu2027Phe, p.Arg2030Gln, p.Arg2107His, p.Cys2137Tyr). The p.Asn1868Ile mutation is present in a loop connecting the V-shaped α-helical hairpin with membrane spanning segment 12 (TM12). Several mutations occur in well-defined motifs crucial for the binding and hydrolysis of ATP. The p.Asn965Ser and p.Glu1087Lys mutations occur in the Walker A (Gly-His-Asn-Gly-Ala-Gly-Lys-Thr) and Walker B (Val-Ile-Leu-Asp-Glu) motifs of NBD1, respectively, and the p.Gly1977Ser mutation is present in the Walker A (Gly-Val-Asn-Gly-Ala-Gly-Lys-Thr) motif of NBD2. The p.Arg2030Gln variant reported to display a mild disease phenotype in compound heterozygous STGD1 patients has been included in our analysis although this variant has yet to be found in a homozygous state.
A ClinVar entry claimed this variant showed "impaired substrate binding capacity and limited substrate release after ATP binding," but it is not found in the text or figures and there is no supplementary data.
Supplementary data. bjophthalmol-2018-312064supp004.pdf
This variant is found on pg 16 in proband 14075. Compound heterozygous for c.6817-2A>C. MEH institute (UK). Said to have Stargardt based on the following criteria: "(1) patients (at least 6 years old) with at least two ABCA4 variants or one ABCA4 variant associated with a typical STGD1 phenotype and (2) presence of a well-defined atrophic lesion with/without flecks at the most recent visit of at least 300 µm in diameter (the total area of all lesions <12 mm2)." No additional details provided
Pt-75Mc.4539 + 2028C > Tp.[= ,Arg1514Leufs*36]c.2453G > Ap.(Gly818Glu)
Case#: Pt 7, male, 60yo at report, onset between 6-49yo, Irish
DiseaseAssertion: Stargardt
FamilyInfo: family 5
CasePresentingHPOs:
CaseHPOFreeText: VA: OD=6/36 OS=6/120, FAF and OCT in figure 2, FAF WRT vascular arcades=beyond, beaten bronze appearance, yellow flecks centrally, peripapillary sparing, central retinal thickness: OD=100 microns OS=117 microns, optical coherence tomography (OCT) atrophy horizontal width: OD=6000 microns OS=5446 microns
CaseNotHPOs:
CaseNotHPOFreeText: bulls eye pattern, flecks peripherally
GenotypingMethod: Target capture NGS of the exons and known pathogenic intronic regions of ABCA4, whole-gene single molecule molecular inversion probe (smMIP) based sequencing of ABCA4 as well as 40 kb of flanking sequence, direct Sanger sequencing, or WGS
PreviouslyPublished: n/a
Variant: c.4539 + 2028C > T p.[= ,Arg1514Leufs*36]; c.2453G> A p.(Gly818Glu)
ClinVar: 99135; 236116
CAID: CA227000; CA10576057
SupplementalData: n/a
Patients older than 60 years or with ocular comorbidities such as diabetic retinopathy, uveitis, or glaucoma were excluded. From the remaining list, subjects for whom high-resolution SD-OCT imaging was available were selected. A review of the patient imaging and medical records was performed to identify those who received a clinical diagnosis of Stargardt macular dystrophy based on their clinical phenotype, including color fundus, infrared, FAF, and fluorescein angiography images and electroretinographic findings. 12
Case#: P3, male, 16yo at report, 9yo at dx, US with Indian ethnicity
DiseaseAssertion: Stargardt
FamilyInfo: n/a
CasePresentingHPOs:
CaseHPOFreeText: BCVA (logMAR)= OD=20/160 (0.90), OS=20/125 (0.80)
CaseNotHPOs:
CaseNotHPOFreeText: ocular comorbidities such as diabetic retinopathy, uveitis, or glaucoma
GenotypingMethod: "genetic testing"
PreviouslyPublished: n/a
Variant: c.2453G>A; c.4532C>A (p.Pro1511His)
ClinVar: 99135
CAID: CA227000
SupplementalData: table 1
The study cohort consisted of 643 individuals of (mostly Eastern) European descent. Of these, 2 ABCA4 mutations were identified in 437 cases (68%), 1 mutation in 117 cases (18%) and 0 mutations in 89 cases (14%) (see online supplementary table 1), leaving ~23% of disease-associated alleles in 32% of patients yet to be identified. Almost all patients with no ABCA4 mutations and ~50% of patients with 1 mutation have been screened by whole exome sequencing to determine if variants in other genes were causal in these cases. All cases, where disease-associated variants in other genes were detected, were excluded from this cohort.
Case#: Case #3483, likely European, 10yo at onset
DiseaseAssertion: ABCA4 disease
FamilyInfo: n/a
CasePresentingHPOs:
CaseHPOFreeText:
CaseNotHPOs:
CaseNotHPOFreeText: foveal sparing
GenotypingMethod: NGS, Sanger
PreviouslyPublished: n/a
Variant: c.2453G>A (p.Gly818Glu); c.4462T>C (p.Cys1488Arg)
ClinVar: 99135
CAID: CA227000
SupplementalData: supplemental table 1
Figure 3: Protein yield and ATP-binding capacity of 37 naturally occurring ABCR variants produced in transiently transfected 293 cells.Membranes were analysed by immunoblotting with affinity-purified anti-ABCR antibodies (top) and photoaffinity labelling with α-32P azido-ATP (bottom). We loaded 1 μg (immunoblotting) or 2.5 μg (azido-ATP labelling) of total membrane protein, as determined by Bradford assay, per track. The mutations that reside in NBD-1 and NBD-2 are indicated above the corresponding lanes. The relative levels of the different variant proteins and the extent of azido-ATP labelling were observed to be highly reproducible in multiple independent experiments. ABCR (large arrowhead); an endogenous 55-kD protein (small arrowhead) serves as an internal control for azido-ATP labelling. Molecular mass standards are shown on the left in kD.
This variant was transfected into HEK 293 cells and appears to show reduced expression and ATP-binding capacity, but no quantities were provided
14F/34320/200, 20/250OU: Severe RPE and choroidal atrophic changes in macula and throughout posterior pole and midperiphery, flecks throughout posterior poleCompound heterozygous: G818E and C1488RSubnormal rod, subnormal cone
Case#: Patient #14, female, 34yo
DiseaseAssertion: Stargardt
FamilyInfo:
CasePresentingHPOs:
CaseHPOFreeText: stage 3, BCVA: OD=20/200 OS=20/250, fundus findings: OU: Severe RPE and choroidal atrophic changes in macula and throughout posterior pole and midperiphery, flecks throughout posterior pole, full field ERG: Subnormal rod, subnormal cone,
CaseNotHPOs:
CaseNotHPOFreeText:
GenotypingMethod: direct sequencing of the ABCA4 gene
PreviouslyPublished:
Variant: Compound heterozygous: G818E and C1488R
ClinVar:
CAID:
SupplementalData:
13. 34/F31.021.06OD−68.3−23.32p.Gly818Glu; p.Cys1488Arg
Case#: Pt 13, 34yo, female
DiseaseAssertion: Stargardt
FamilyInfo: n/a
CasePresentingHPOs:
CaseHPOFreeText: stage 3 (resorbed flecks), logMAR acuity: OD=1.02 OS 1.06, FST Rod Blue Stimulus (dB) OD= −68.3, FST Cone Red stimulus (dB) OD=−23.3, FST Group 2 (elevated cone and normal rod FST thresholds)
CaseNotHPOs:
CaseNotHPOFreeText:
GenotypingMethod:
PreviouslyPublished:
Variant: p.Gly818Glu; p.Cys1488Arg
ClinVar: 99135
CAID: CA227000
SupplementalData: n/a
Supplementary data. bjophthalmol-2018-312064supp004.pdf
This variant is found on pg 2 in proband 11019. Compound heterozygous for c.4532C>A, (p.Pro1511His). JHU institute (US). Said to have Stargardt based on the following criteria: "(1) patients (at least 6 years old) with at least two ABCA4 variants or one ABCA4 variant associated with a typical STGD1 phenotype and (2) presence of a well-defined atrophic lesion with/without flecks at the most recent visit of at least 300 µm in diameter (the total area of all lesions <12 mm2)." No additional details provided
G818EER51 ± 1363 ± 5111 ± 825 ± 312 ± 32Moderate/Severe
When expressed in transfected HEK293T cells and quantified by Western blotting, this variant was in the range of 40%-52%. This variant has a basal ATPase activity of 63% ± 5% compared to WT (100%) and was categorized as class 2 (partial reduction in expression and basal ATPase activity that was modestly stimulated by N-Ret-PE) with a moderate/severe predicted severity.
In Mexican patients, p.A1773V and p.G818E were identified in 17% and 15%, respectively, of the total mutant alleles.
This variant was mentioned in reference to a previous publication. PMID: 23419329
Sixty-six individuals representing 54 families were studied (Supplementary Material, Table S1). All individuals were found to harbor two ABCA4 variants likely to cause the retinal disease (18,20–26). In 40 families (74%), independent segregation of the two alleles was demonstrated. The ages at the time of their first visit ranged from 9 to 74 years (mean = 35.9, median = 35.2 years); in the majority of individuals (36/66=55%), data were available from a second visit that occurred on average 8.7 years (range=2–20 years, median = 6.9 years) after the first visit.
Case#: Patient #35, male, 35yo at report, 14yo at onset,
DiseaseAssertion: STGD
FamilyInfo: family 30, segregation was noted as "yes" but no other details provided
CasePresentingHPOs:
CaseHPOFreeText:
CaseNotHPOs:
CaseNotHPOFreeText:
GenotypingMethod:
PreviouslyPublished: n/a
Variant: allele 1: A1038V;L541P allele 2: G818E
ClinVar: 99135
CAID: CA227000
SupplementalData: supplemental table 1