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 label mismatch: IDUA vs undefined
  • 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.123G>A (p.Trp41Ter)

CA355945567

2734632 (ClinVar)

Gene: IDUA (HGNC:3425)
Condition: mucopolysaccharidosis type 1 (MONDO:0001586)
Inheritance Mode: Autosomal recessive inheritance
UUID: 9e526aa0-5e27-46f8-9ef3-5e53aed401d8
Approved on: 2025-04-07
Published on: 2025-05-04

HGVS expressions

NM_000203.5(IDUA):c.123G>A (p.Trp41Ter)
NM_000203.5:c.123G>A
NC_000004.12:g.987207G>A
CM000666.2:g.987207G>A
NC_000004.11:g.980995G>A
CM000666.1:g.980995G>A
NC_000004.10:g.970995G>A
NG_008103.1:g.5211G>A
NG_033042.1:g.11230C>T
ENST00000247933.9:c.123G>A
ENST00000514224.2:c.123G>A
ENST00000247933.8:c.123G>A
ENST00000398520.6:c.576+3921C>T
ENST00000502910.5:c.123G>A
ENST00000504568.5:c.121G>A
ENST00000506561.5:n.132G>A
ENST00000508168.5:n.142G>A
ENST00000514698.5:n.164G>A
ENST00000622731.4:c.576+3921C>T
NM_000203.4:c.123G>A
NM_134425.2:c.576+3921C>T
NR_110313.1:n.211G>A
NM_134425.3:c.576+3921C>T
NM_134425.4:c.576+3921C>T
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Pathogenic

Met criteria codes 3
PP4_Moderate PM2_Supporting PVS1
Not Met criteria codes 1
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. c.123G>A (p.Trp41Ter) variant in IDUA is a nonsense variant predicted to cause a premature stop codon in biologically-relevant-exon 1 out of 14, leading to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1). This variant has been detected in at least one individual with Hurler syndrome, presenting with IDUA deficiency within the affected range, increased excretion of urinary dermatan sulfate and heparan sulfate, and clinical features specific to MPS I including Macrocephaly, joint stiffness, Mongolian macula, hepatosplenomegaly, hernia, cardiac disease, and airway obstruction (PMID 21480867) (PP4_moderate). This individual is compound heterozygous for the variant and c.300-1G>C, p.(?). The allelic data for this patient will be used to support the classification of c.300-1G>C and is not included here in order to avoid circular logic. The highest population minor allele frequency in gnomAD v4.1.0 is 8.889e-7 (1/1,124,963 alleles) in the Non-Finnish European 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: 2734632). 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 moderate, PM2 supporting). (Classification approved by the ClinGen Lysosomal Diseases Variant Curation Expert Panel on April 7, 2025)
Met criteria codes
PP4_Moderate
This variant has been detected in at least one individual with Hurler syndrome, presenting with IDUA deficiency within the affected range, increased excretion of urinary dermatan sulfate and heparan sulfate, and clinical features specific to MPS I including macrocephaly, joint stiffness, Mongolian macula, hepatosplenomegaly, hernia, cardiac disease, and airway obstruction (PMID 21480867) (PP4_moderate).
PM2_Supporting
The highest population minor allele frequency in gnomAD v4.1.0 is 8.889e-7 (1/1,124,963 alleles) in the Non-Finnish European 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. c.123G>A (p.Trp41Ter) variant in IDUA is a nonsense variant predicted to cause a premature stop codon in biologically-relevant-exon 1 out of 14, leading to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1).
Not Met criteria codes
PM3
This individual is compound heterozygous for c.123G>A (p.Trp41Ter) and c.300-1G>C, p.(?). The allelic data for this patient will be used to support the classification of c.300-1G>C and is not included here in order to avoid circular logic.
Curation History
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