Supplementary TableS10
This variant is listed for Stargardt DNAID#067322 in trans with c.5603A>T p.(Asn1868Ile). No phenotype information provided.
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Supplementary MaterialsSupplementary information41598_2017_11211_MOESM1_ESM.xlsx (63K)
This paper is flagged in Mastermind as containing this variant. The rs12720449 ID is mentioned in the supplemental info under the controls tab, but the specific variant is not listed
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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
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Screening of reported pathogenic variants in ABCA4 for Stargardt (STGD) The disease prevalence of STGD is estimated as 1 in 10000 individuals4. It has been estimated that about 70% of STGD patients carry variants in ABCA45. Therefore, this represents the scenario of a recessive disease with a relatively homogeneous genetic cause. We screened 945 reported pathogenic variants in ABCA4 genes collected in HGMD. Among them, 11 variants are likely benign, as their population AF in is higher than 0.7% (1/20000‾‾‾‾‾‾‾‾√)<math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline" id="M11"><mrow><mrow><mo>(</mo><mrow><msqrt><mrow><mn>1</mn><mo>/</mo><mn>20000</mn></mrow></msqrt></mrow><mo>)</mo></mrow></mrow></math>, the cutoff based on STGD disease prevalence, therefore were excluded from further analysis. The remaining 934 variants were subjected to our test model. As a result, 26 variants with the AF in the range of 0.46% to 0.03% were identified as likely benign (Binomial test1, Bonferroni correction p-value ≤ 0.05/934 and test2 Bonferroni correction p-value > 0.05/934) (Figure 3A).
This variant is reported in Table S6, but only location, predictions, frequencies, etc are reported for it, not cases.
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Screening of reported pathogenic variants in ABCA4 for Stargardt (STGD) The disease prevalence of STGD is estimated as 1 in 10000 individuals4. It has been estimated that about 70% of STGD patients carry variants in ABCA45. Therefore, this represents the scenario of a recessive disease with a relatively homogeneous genetic cause. We screened 945 reported pathogenic variants in ABCA4 genes collected in HGMD. Among them, 11 variants are likely benign, as their population AF in is higher than 0.7% (1/20000‾‾‾‾‾‾‾‾√)<math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline" id="M11"><mrow><mrow><mo>(</mo><mrow><msqrt><mrow><mn>1</mn><mo>/</mo><mn>20000</mn></mrow></msqrt></mrow><mo>)</mo></mrow></mrow></math>, the cutoff based on STGD disease prevalence, therefore were excluded from further analysis. The remaining 934 variants were subjected to our test model. As a result, 26 variants with the AF in the range of 0.46% to 0.03% were identified as likely benign (Binomial test1, Bonferroni correction p-value ≤ 0.05/934 and test2 Bonferroni correction p-value > 0.05/934) (Figure 3A).
This variant is reported in Table S6, but only location, predictions, frequencies, etc are reported for it, not cases.
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See Supplementary Table S2 for a complete genotypic glossary of the cohort.
Case#: Patients were identified from the inherited retinal disease (IRD) database at UC San Diego (UCSD).
DiseaseAssertion: RP with macular edema
FamilyInfo:
CasePresentingHPOs:
CaseHPOFreeText: Dx of RP based on "a history of progressive peripheral vision loss or nyctalopia, and ocular examination findings of RP including bone spicule pigmentation, disc pallor and attenuated vessels and genetic confirmation."
CaseNotHPOs:
CaseNotHPOFreeText:
GenotypingMethod: Next-generation sequencing (NGS), exome sequencing, and/or targeted Sanger sequencing were the primary genetic testing approaches.
PreviouslyPublished: PMID:10206579 is referenced but it seems a reference to the variant and not the proband
Variant: c.6383A>G (p.His2128Arg); c.3G>T (p.Met1?). phase unknown
ClinVar: 99455
CAID: CA227399
SupplementalData: Variant is found in table S2
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