p.Ile270Ser
This variant is mentioned in reference to previously published papers that report IEMs
5 Matching Annotations
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www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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www-sciencedirect-com.libproxy.lib.unc.edu www-sciencedirect-com.libproxy.lib.unc.edu
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I270S0.0090544.7Severe[31]HurlerR628X
This variant was mentioned as being previously published (PMID: 16435195). Structural changes for this variant were analyzed by calculating RMSD and predicted this variant to result in a severe phenotype. However, this type of prediction is not used by the LD VCEP.
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www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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I270Ssevere
This paper uses in silico predictors to evaluate variants. Prediction is severe for this variant.
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pubmed.ncbi.nlm.nih.gov pubmed.ncbi.nlm.nih.gov
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The results indicated that large structural changes had occurred in the core region in the severe MPS I group and small ones on the molecular surface in the attenuated MPS I group.
Article is a PDF, so annotating here. This paper created structural models to predict the phenotype. This variant is predicted to cause a severe phenotype, but this model is not used for PS3 or any other codes.
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link-springer-com.libproxy.lib.unc.edu link-springer-com.libproxy.lib.unc.edu
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The patient in family 2 who also had the Hurler phenotype was heteroallelic for the novel missense mutation I270S and the previously reported nonsense mutation R628X.
Article is a PDF, so annotating here.
Case#: Family 2, Proband 3, Tunisia (Mednine), female, death at 5yo
DiseaseAssertion: MPS1, Hurler
FamilyInfo: Offspring of consanguineous marriage between first cousins. Variants were said to be found in parents as well. Mother had I270S and father had R628X
CasePresentingHPOs:
CaseHPOFreeText: Leukocyte IDUA activity= <0.1% of normal
CaseNotHPOs:
CaseNotHPOFreeText:
CasePreviousTesting: n/a
GenotypingMethod: PCR sequencing with possible confirmation by restriction enzyme digestion on a second PCR product.
PreviouslyPublished: n/a
Variant: c.1882C>T p.(R628X) and c.809T>G p.(I270S) compound heterozygous. Confirmed in trans. Also has the following polymorphisms: R105Q, N181N, T410T, V454I, IVS8+2573insC.
ClinVar: 550421
CAID: CA2802462; CA355962322
gnomAD: The highest population minor allele frequency in gnomAD v4.1.0. is 0.00005038 (2/39700 alleles) in the East Asian population, which is lower than the ClinGen Lysosomal Diseases VCEP’s threshold for PM2_Supporting (<0.00025), meeting this criterion (PM2_Supporting).
SupplementalData: n/a
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