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.876del (p.Asp292fs)

CA658657370

456720 (ClinVar)

Gene: IDUA
Condition: mucopolysaccharidosis type 1
Inheritance Mode: Autosomal recessive inheritance
UUID: 0ddf0e4b-c28e-40d3-85ce-e431096b7788
Approved on: 2024-12-05
Published on: 2025-03-19

HGVS expressions

NM_000203.5:c.876delC
NM_000203.5:c.876del
NM_000203.5(IDUA):c.876del (p.Asp292fs)
NC_000004.12:g.1002065del
CM000666.2:g.1002065del
NC_000004.11:g.995853del
CM000666.1:g.995853del
NC_000004.10:g.985853del
NG_008103.1:g.20069del
ENST00000247933.9:c.876del
ENST00000514224.2:c.876del
ENST00000652070.1:n.932del
ENST00000247933.8:c.876del
ENST00000514192.5:c.693del
ENST00000514224.1:c.480del
ENST00000514698.5:n.876del
NM_000203.4:c.876del
NR_110313.1:n.964del
NM_001363576.1:c.480del
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Pathogenic

Met criteria codes 4
PVS1 PM3_Supporting PP4_Moderate PM2_Supporting

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.876del (p.Asp292GlufsTer25) variant in IDUA is a frameshift variant predicted to cause a premature stop codon, leading to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1). The variant has been reported in two individuals with clinical features consistent with MPS I, one of whom also had documented laboratory values showing deficiency leukocyte IDUA activity and elevated urine GAGs prior to initiation of treatment with enzyme replacement therapy (PMID: 35848209) (PP4). One of these individuals is compound heterozygous for the variant (labeled as 964del in the publication, using older numbering) and a variant in IDUA that has been classified as pathogenic by the ClinGen Lysosomal Diseases VCEP, c.1205G>A (p.Trp402Ter) (ClinVar Variation ID: 11908); the phase was not confirmed (PMID: 7951228, 0.5 points). Another patient is compound heterozygous for the variant and c.1499A>G (p.Gln500Arg) (PMID: 35848209). The allelic data from this patient will be used in the classification of p.Gln500Arg 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 0.00001280 (15/1172250 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). There is a ClinVar entry for this variant (Variation ID: 456720). In summary, this variant meets the criteria to be classified as pathogenic for mucopolysaccharidosis type I. IDUA-specific ACMG/AMP criteria met, 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 December 5, 2024)
Met criteria codes
PVS1
The NM_000203.5:c.876del (p.Asp292GlufsTer25) variant in IDUA is a frameshift variant predicted to cause a premature stop codon in exon 7 out of 14 exons, leading to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1).
PM3_Supporting
One individual is compound heterozygous for the variant (labeled as 964del in the publication, using older numbering) and a variant in IDUA that has been classified as pathogenic by the ClinGen Lysosomal Diseases VCEP, c.1205G>A (p.Trp402Ter) (ClinVar Variation ID: 11908); the phase was not confirmed (PMID: 7951228, 0.5 points). Another patient is compound heterozygous for the variant and c.1499A>G (p.Gln500Arg) (PMID: 35848209). The allelic data from this patient will be used in the classification of p.Gln500Arg and is not included here to avoid circular logic. Total 0.5 points (PM3_Supporting).
PP4_Moderate
The variant has been reported in two individuals with clinical features consistent with MPS1, one of whom also had documented laboratory values showing deficiency leukocyte IDUA activity and elevated urine GAGs prior to initiation of treatment with enzyme replacement therapy (PMID: 35848209) (PP4).
PM2_Supporting
The highest population minor allele frequency in gnomAD v4.1.0 is 0.00001280 (15/1172250 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).
Curation History
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