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.1855C>T (p.Arg619Ter)

CA2802455

280976 (ClinVar)

Gene: IDUA
Condition: mucopolysaccharidosis type 1
Inheritance Mode: Autosomal recessive inheritance
UUID: a1efaa97-f0ac-4983-ae5c-53e42753d7af
Approved on: 2024-12-06
Published on: 2025-06-07

HGVS expressions

NM_000203.5:c.1855C>T
NM_000203.5(IDUA):c.1855C>T (p.Arg619Ter)
NC_000004.12:g.1004286C>T
CM000666.2:g.1004286C>T
NC_000004.11:g.998074C>T
CM000666.1:g.998074C>T
NC_000004.10:g.988074C>T
NG_008103.1:g.22290C>T
ENST00000247933.9:c.1855C>T
ENST00000514224.2:c.1855C>T
ENST00000652070.1:n.1911C>T
ENST00000247933.8:c.1855C>T
ENST00000514224.1:c.1459C>T
ENST00000514698.5:n.1966C>T
NM_000203.4:c.1855C>T
NR_110313.1:n.1947C>T
NM_001363576.1:c.1459C>T
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Pathogenic

Met criteria codes 4
PP4 PM3_Very Strong PVS1_Moderate PM2_Supporting
Not Met criteria codes 2
PS3 BS3

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.1855C>T (p.Arg619Ter) variant in IDUA is a nonsense variant predicted to cause a premature stop codon in the last exon of the gene and therefore to escape nonsense mediated decay. Less than 10% of the protein is predicted to be removed. (PVS1_Moderate; PMID: 24480078). At least 4 patients with this variant had documented IDUA deficiency within the affected range in leukocytes or plasma, and clinical features specific to MPS I including dysostosis multiplex, hepatosplenomegaly, arthropathy, and corneal involvement (PP4). This variant has been detected in at least 12 individuals with MPS I. Of those individuals, 6 were compound heterozygous for the variant and a pathogenic or likely pathogenic variant (Variants: 1163C>G (p.Thr388Arg), 1598C>G (p.Pro533Arg), 1205G>A (p.Trp402Ter), 386-2A>G, 208C>T (p.Gln70Ter)) and none of those were confirmed in trans (PMIDs: 28752568, 11735025). 6 individuals were homozygous for the variant (PMID: 28752568, PMID: 27146977) (PM3_very strong). The highest population minor allele frequency in gnomAD v4.1.0. is 0.00002881 (34/1179960 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: 280976, 2 star review status) with 6 submitters classifying the variant as pathogenic. 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): PM3_very strong, PVS1_moderate, PP4, PM2_supporting. (Classification approved by the ClinGen Lysosomal Diseases Variant Curation Expert Panel on December 6, 2024)
Met criteria codes
PP4
At least 4 patients with this variant had documented IDUA deficiency within the affected range in leukocytes or plasma, and clinical features specific to MPS I including dysostosis multiplex, hepatosplenomegaly, arthropathy, and corneal involvement (PP4).
PM3_Very Strong
This variant has been detected in at least 12 individuals with MPS I. Of those individuals, 6 were compound heterozygous for the variant and a pathogenic or likely pathogenic variant (Variants: 1163C>G (p.Thr388Arg), 1598C>G (p.Pro533Arg), 1205G>A (p.Trp402Ter), 386-2A>G, 208C>T (p.Gln70Ter)) and none of those were confirmed in trans (3 points; PMIDs: 28752568, 11735025). 6 individuals were homozygous for the variant (1 point, PMID: 28752568, PMID: 27146977). Total 4 points (PM3_VeryStrong).
PVS1_Moderate
The NM_000203.5:c.1855C>T (p.Arg619Ter) variant in IDUA is a nonsense variant predicted to cause a premature stop codon in the last exon of the gene and therefore to escape nonsense mediated decay. Less than 10% of the protein is predicted to be removed. (PVS1_Moderate).
PM2_Supporting
The highest population minor allele frequency in gnomAD v4.1.0. is 0.00002881 (34/1179960 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).
Not Met criteria codes
PS3
To our knowledge, the results of functional assays have not been reported for this variant.
BS3
To our knowledge, the results of functional assays have not been reported for this variant.
Curation History
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