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


Variant: NM_000203.5(IDUA):c.606C>A (p.Tyr202Ter)

CA355961907

552333 (ClinVar)

Gene: IDUA
Condition: mucopolysaccharidosis type 1
Inheritance Mode: Autosomal recessive inheritance
UUID: e7a73bf2-fa27-4a07-9320-526de1dcc814
Approved on: 2025-01-06
Published on: 2025-03-12

HGVS expressions

NM_000203.5:c.606C>A
NM_000203.5(IDUA):c.606C>A (p.Tyr202Ter)
NC_000004.12:g.1001695C>A
CM000666.2:g.1001695C>A
NC_000004.11:g.995483C>A
CM000666.1:g.995483C>A
NC_000004.10:g.985483C>A
NG_008103.1:g.19699C>A
ENST00000247933.9:c.606C>A
ENST00000514224.2:c.606C>A
ENST00000652070.1:n.662C>A
ENST00000247933.8:c.606C>A
ENST00000502910.5:c.465C>A
ENST00000504568.5:c.566C>A
ENST00000509948.5:c.399C>A
ENST00000514192.5:c.423C>A
ENST00000514224.1:c.210C>A
ENST00000514698.5:n.506C>A
NM_000203.4:c.606C>A
NR_110313.1:n.694C>A
NM_001363576.1:c.210C>A
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Pathogenic

Met criteria codes 4
PVS1 PM2_Supporting PP4 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.606C>A (p.Tyr202Ter) variant in IDUA is a nonsense variant predicted to cause a premature stop codon in biologically-relevant exon 6 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 3 individuals with MPS I. Of those individuals, all 3 were compound heterozygous for the variant and a pathogenic variant (c.979G>C p.A327P; c.208C>T p.Q70X; c.1205G>A p.W402X) and none of those were confirmed in trans (PMIDs: 27392569, 22976768, clinical lab; PM3). At least 1 patient with this variant had clinical features specific to MPS I including dysostosis multiplex and arthropathy (PMID: 27392569; PP4). The highest population minor allele frequency in gnomAD v4.0 is 0.000005089 (6/1179008 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). To our knowledge, the results of functional assays have not been reported for this variant. There is a ClinVar entry for this variant (Variation ID: 552333, 2 star review status) with 5 submitters classifying the variant as pathogenic. In summary, this variant meets the criteria to be classified as pathogenic for MPS I based on the ACMG/AMP criteria applied, as specified by the ClinGen Lysosomal Diseases Variant Curation Expert panel (Specifications Version 1.0.0): PVS1, PM3, PP4, PM2_Supporting. (Classification approved by the ClinGen Lysosomal Diseases Variant Curation Expert Panel on January 6, 2025)
Met criteria codes
PVS1
The NM_000203.5:c.606C>A (p.Tyr202Ter) variant in IDUA is a nonsense variant predicted to cause a premature stop codon in biologically-relevant exon 6 out of 14, leading to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1).
PM2_Supporting
The highest population minor allele frequency in gnomAD v4.0 is 0.000005089 (6/1179008 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).
PP4
At least 1 patient with this variant had clinical features specific to MPS I including dysostosis multiplex and arthropathy (PMID: 27392569; PP4). Per VCEP expert discussion, these probands were reported by reputable groups and, although our specific PP4 criteria are not explicitly met, PP4 will be applied to this variant.
PM3
This variant has been detected in at least 3 individuals with MPS I. Of those individuals, all 3 were compound heterozygous for the variant and a pathogenic variant (c.979G>C p.A327P; c.208C>T p.Q70X; c.1205G>A p.W402X) and none of those were confirmed in trans (PM3=1.5 points; PMIDs: 27392569, 22976768, clinical lab; PM3). Of note, this variant appears to be associated with a haplotype where it is always seen in cis with M133I.
Curation History
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