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  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data


Variant: NM_000203.5(IDUA):c.1728-1G>C

CA355965306

556064 (ClinVar)

Gene: IDUA
Condition: mucopolysaccharidosis type 1
Inheritance Mode: Autosomal recessive inheritance
UUID: 9bf5fbe0-8c38-4b1e-a07d-f5f00664016f
Approved on: 2024-12-05
Published on: 2025-03-03

HGVS expressions

NM_000203.5:c.1728-1G>C
NM_000203.5(IDUA):c.1728-1G>C
NC_000004.12:g.1004011G>C
CM000666.2:g.1004011G>C
NC_000004.11:g.997799G>C
CM000666.1:g.997799G>C
NC_000004.10:g.987799G>C
NG_008103.1:g.22015G>C
ENST00000247933.9:c.1728-1G>C
ENST00000514224.2:c.1728-1G>C
ENST00000652070.1:n.1784-1G>C
ENST00000247933.8:c.1728-1G>C
ENST00000514224.1:c.1332-1G>C
ENST00000514698.5:n.1839-1G>C
NM_000203.4:c.1728-1G>C
NR_110313.1:n.1820-1G>C
NM_001363576.1:c.1332-1G>C
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Pathogenic

Met criteria codes 4
PP4 PM2_Supporting PVS1 PM3

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Lysosomal Diseases Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for IDUA Version 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Lysosomal Diseases VCEP
The NM_000203.5:c.1728-1G>C variant in IDUA occurs within the canonical splice acceptor site of intron 12. It is predicted to cause skipping of biologically-relevant exon 13 out of 14, resulting in a frameshift leading to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1). At least 3 patients with this variant had documented IDUA deficiency within the affected range and urinary GAG elevation above normal range (PP4; PMID: 31194252). This variant has been detected in at least 2 individuals with MPS I. Of those individuals, both were compound heterozygous for the variant and a pathogenic variant (Q70X; W402X) and neither of those were confirmed in trans (PM3; PMID: 31194252). The highest population minor allele frequency in gnomAD v4.0. is 0.00001612 (19/1178792 alleles) in the European (non-Finnish) population, which is lower than the ClinGen Lysosomal Diseases VCEP’s threshold for PM2_Supporting (<0.00025), meeting this criterion (PM2_Supporting). In summary, this variant meets the criteria to be classified as pathogenic for MPS I based on the IDUA-specific ACMG/AMP criteria applied, as specified by the ClinGen Lysosomal Diseases Variant Curation Expert panel (Specifications Version 1.0): PVS1, PP4, PM3, PM2_Supporting. (Classification approved by the ClinGen Lysosomal Diseases Variant Curation Expert Panel on December 5, 2024)
Met criteria codes
PP4
At least 3 patients with this variant had documented IDUA deficiency within the affected range and urinary GAG elevation above normal range (PP4; PMID: 31194252).
PM2_Supporting
The highest population minor allele frequency in gnomAD v4.0. is 0.00001612 (19/1178792 alleles) in the European (non-Finnish) population, which is lower than the ClinGen Lysosomal Diseases VCEP’s threshold for PM2_Supporting (<0.00025), meeting this criterion (PM2_Supporting).
PVS1
The NM_000203.5:c.1728-1G>C variant in IDUA occurs within the canonical splice acceptor site of intron 12. It is predicted to cause skipping of biologically-relevant exon 13 out of 14, resulting in a frameshift leading to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1).
PM3
This variant has been detected in at least 2 individuals with MPS I. Of those individuals, both were compound heterozygous for the variant and a pathogenic variant (Q70X; W402X) and neither of those were confirmed in trans (PM3= 1 point; PM3; PMID: 31194252).
Curation History
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