Variant: NM_001363576.1:c.105C>A

CA355961650

Gene: IDUA

Condition: mucopolysaccharidosis type 1

Inheritance Mode: Autosomal recessive inheritance

UUID: abe2b5ba-191b-4130-b07e-261128d65140

Approved on: 2025-04-07

Published on: 2025-04-07

HGVS expressions

NM_001363576.1:c.105C>A
NC_000004.12:g.1001475C>A
CM000666.2:g.1001475C>A
NC_000004.11:g.995263C>A
CM000666.1:g.995263C>A
NC_000004.10:g.985263C>A
NG_008103.1:g.19479C>A
ENST00000247933.9:c.501C>A
ENST00000514224.2:c.501C>A
ENST00000652070.1:n.557C>A
ENST00000247933.8:c.501C>A
ENST00000502910.5:c.360C>A
ENST00000504568.5:c.461C>A
ENST00000509948.5:c.294C>A
ENST00000514192.5:c.318C>A
ENST00000514224.1:c.105C>A
ENST00000514698.5:n.401C>A
NM_000203.4:c.501C>A
NR_110313.1:n.589C>A
NM_000203.5:c.501C>A

Pathogenic

• Met criteria codes: PVS1 PP4_Moderate PM2_Supporting PM3_Supporting

Expert Panel

Lysosomal Diseases VCEP

Criteria Specification Information

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

Evidence submitted by expert panel

Lysosomal Diseases VCEP

The NM_000203.5:c.501C>A (p.Tyr167Ter) variant in IDUA is a nonsense variant predicted to cause a premature stop codon in biologically-relevant-exon 5 out of 14, leading to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1). Two patients with the variant have been reported to have clinical features consistent with MPS and both with IDUA deficiency, and one is reported to have elevated urinary dermatan sulfate and heparan sulfate although no values to reference range were provided (PMID: 11735025, 19396826) (PP4). One of these individuals is compound heterozygous for the variant and another variant in IDUA that has been classified as pathogenic by the ClinGen LD VCEP, c.208C>T (p.Gln70Ter) (ClinVar Variation ID: 11909), phase not confirmed (PMID: 19396826, 0.5 points). The other patient is compound heterozygous for the variant and c.614G>A (p.Cys205Tyr) (PMID: 11735025). The allelic data from this patient will be used in the assessment of p.Cys205Tyr and is not included here to avoid circular logic. Total 0.5 points (PM3_Supporting). The highest population minor allele frequency in gnomAD v4.1.0 is 8.476e-7 (1/1179740 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 mucopolysaccharidosis type I. IDIA-specific ACMG/AMP criteria applied, as specified by the ClinGen Lysosomal Diseases Variant Curation Expert Panel (Specifications Version 1.0.0): PVS1, PP4, PM2_Supporting, PM3_Supporting. (Classification approved by the ClinGen Lysosomal Diseases Variant Curation Expert Panel on April 7, 2025).

Met criteria codes

• PVS1: The NM_000203.5:c.501C>A (p.Tyr167Ter) variant in IDUA is a nonsense variant predicted to cause a premature stop codon in biologically-relevant-exon 5 out of 14, leading to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1).
• PP4_Moderate: Two patients with the variant have been reported to have clinical features consistent with MPS I and both with IDUA deficiency, and one is reported to have elevated urinary dermatan sulfate and heparan sulfate although no values to reference range were provided (PMID: 11735025, 19396826) (PP4).
• PM2_Supporting: The highest population minor allele frequency in gnomAD v4.1.0 is 8.476e-7 (1/1179740 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).
• PM3_Supporting: One individual is compound heterozygous for the variant and another variant in IDUA that has been classified as pathogenic by the ClinGen LD VCEP, c.208C>T (p.Gln70Ter) (ClinVar Variation ID: 11909), phase not confirmed (PMID: 19396826, 0.5 points). Another patient is compound heterozygous for the variant and c.614G>A (p.Cys205Tyr) (PMID: 11735025). The allelic data from this patient will be used in the assessment of p.Cys205Tyr and is not included here to avoid circular logic. Total 0.5 points (PM3_Supporting).