The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_000203.5(IDUA):c.895G>T (p.Glu299Ter)

CA355962511

987878 (ClinVar)

Gene: IDUA (HGNC:3425)
Condition: mucopolysaccharidosis type 1 (MONDO:0001586)
Inheritance Mode: Autosomal recessive inheritance
UUID: 827b53ba-aaa5-414e-93ca-377fab47a169
Approved on: 2025-06-16
Published on: 2025-07-18

HGVS expressions

NM_000203.5:c.895G>T
NM_000203.5(IDUA):c.895G>T (p.Glu299Ter)
NC_000004.12:g.1002084G>T
CM000666.2:g.1002084G>T
NC_000004.11:g.995872G>T
CM000666.1:g.995872G>T
NC_000004.10:g.985872G>T
NG_008103.1:g.20088G>T
ENST00000247933.9:c.895G>T
ENST00000514224.2:c.895G>T
ENST00000652070.1:n.951G>T
ENST00000247933.8:c.895G>T
ENST00000514224.1:c.499G>T
ENST00000514698.5:n.895G>T
NM_000203.4:c.895G>T
NR_110313.1:n.983G>T
NM_001363576.1:c.499G>T
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Pathogenic

Met criteria codes 4
PP4 PM3 PM2_Supporting PVS1

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(IDUA):c.895G>T (p.Glu299Ter) variant in IDUA is a nonsense variant predicted to cause a premature stop codon in biologically-relevant exon 7 out of 14, leading to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1). At least 2 patients with this variant had documented IDUA deficiency within the affected range in leukocytes and clinical features specific to MPS I including dysostosis multiplex, hepatosplenomegaly, arthropathy, and corneal involvement (PMIDs: 16438163, 27146977) (PP4). Of those individuals, one was compound heterozygous for the variant and another variant in IDUA that has been classified as pathogenic for MPS I by the ClinGen LD VCEP, c.223G>A (p.Ala75Thr) (ClinVar Variation ID: 222993); the phase was not confirmed (0.5 points; PMID: 27146977). One individual was homozygous for the variant (ClinVar SCV002562742.2) (0.5 points). Total 1 point (PM3). Another patient was compound heterozygous for the variant and c.164dup (PMID: 16438163). The allelic data for this patient will be used to support the classification of c.164dup and is not included here in order to avoid circular logic. The highest population minor allele frequency in gnomAD v4.1.0. is 0.000023 (2/86636 alleles) in the South Asian population, which is lower than the ClinGen Lysosomal Diseases VCEP’s threshold for PM2_Supporting (<0.00025), meeting this criterion (PM2_Supporting). There is a ClinVar entry for this variant (Variation ID: 987878). 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 1.0.0): PVS1, PP4, PM3, PM2_Supporting. (Classification approved by the ClinGen Lysosomal Diseases Variant Curation Expert Panel on June 16, 2025)
Met criteria codes
PP4
At least 2 patients with this variant had documented IDUA deficiency within the affected range in leukocytes and clinical features specific to MPS I including dysostosis multiplex, hepatosplenomegaly, arthropathy, and corneal involvement (PMIDs: 16438163, 27146977) (PP4).
PM3
This variant has been detected in at least 2 individuals with MPS I. Of those individuals, 1 was compound heterozygous for the variant and another variant in IDUA that has been classified as pathogenic for MPS I by the ClinGen LD VCEP, c.223G>A (p.Ala75Thr) (ClinVar Variation ID: 222993); the phase was not confirmed (0.5 points; PMID: 27146977). One individual was homozygous for the variant (ClinVar SCV002562742.2) (0.5 points). Total 1 point (PM3). Another patient was compound heterozygous for the variant and c.164dup (PMID: 16438163). The allelic data for this patient will be used to support the classification of c.164dup and is not included here in order to avoid circular logic.
PM2_Supporting
The highest population minor allele frequency in gnomAD v4.1.0. is 0.000023 (2/86636 alleles) in the South Asian 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(IDUA):c.895G>T (p.Glu299Ter) variant in IDUA is a nonsense variant predicted to cause a premature stop codon in biologically-relevant exon 7 out of 14, leading to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1).
Curation History
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