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
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Variant: NM_000203.5(IDUA):c.956C>T (p.Ala319Val)

CA2802126

1683230 (ClinVar)

Gene: IDUA (HGNC:3425)
Condition: mucopolysaccharidosis type 1 (MONDO:0001586)
Inheritance Mode: Autosomal recessive inheritance
UUID: 36f5b707-fb05-4fe2-8fc2-8494a52a3188
Approved on: 2025-08-08
Published on: 2025-09-16

HGVS expressions

NM_000203.5:c.956C>T
NM_000203.5(IDUA):c.956C>T (p.Ala319Val)
NC_000004.12:g.1002145C>T
CM000666.2:g.1002145C>T
NC_000004.11:g.995933C>T
CM000666.1:g.995933C>T
NC_000004.10:g.985933C>T
NG_008103.1:g.20149C>T
ENST00000247933.9:c.956C>T
ENST00000514224.2:c.956C>T
ENST00000652070.1:n.1012C>T
ENST00000247933.8:c.956C>T
ENST00000514224.1:c.560C>T
ENST00000514698.5:n.956C>T
NM_000203.4:c.956C>T
NR_110313.1:n.1044C>T
NM_001363576.1:c.560C>T
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Likely Pathogenic

Met criteria codes 5
PM3_Supporting PP4 PP3_Moderate PM2_Supporting PS3_Supporting

Evidence Links 1

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.956C>T variant in IDUA is a missense variant predicted to cause substitution of alanine by valine at amino acid 319 (p.Ala319Val). One patient from Pakistan, homozygous for the variant, was diagnosed with attenuated MPS I (described as having Scheie syndrome) and low IDUA activity (PMID: 11735025) (PP4, PM3_supporting). The highest population minor allele frequency in gnomAD v4.1.0 is 0.0001673 (1/5976 alleles) in the Middle Eastern population, which is lower than the ClinGen Lysosomal Diseases VCEP’s threshold for PM2_Supporting (<0.00025), meeting this criterion (PM2_Supporting). When expressed in COS cells, the activity of the variant was indistinguishable from that of untransfected COS cells (PMID: 11735025) (PS3_Supporting). The computational predictor REVEL gives a score of 0.896 which is above the threshold of 0.773, evidence that correlates with impact to IDUA function at the moderate level based on the specifications of the ClinGen Lysosomal Diseases VCEP (PMID: 36413997) (PP3_Moderate). There is a ClinVar entry for this variant (Variation ID: 1683230). In summary, this variant meets the criteria to be classified as likely pathogenic for mucopolysaccharidosis type I based on the IDUA-specific ACMG/AMP criteria applied, as specified by the ClinGen Lysosomal Diseases Expert Panel (Specifications Version 1.0.0): PP3_Moderate, PP4, PS3_Supporting, PM2_Supporting, PM3_Supporting. (Classification approved by the ClinGen Lysosomal Diseases Expert Panel, August 8, 2025)
Met criteria codes
PM3_Supporting
This variant has been detected in at least 01 individuals with MPS I. This individual was homozygous for the variant (0.5 points, PMID: 11735025) (PM3_supporting).
PP4
One patient from Pakistan, homozygous for the variant, was diagnosed with attenuated MPS I (described as having Scheie syndrome) and low IDUA activity (PMID: 11735025) (PP4)
PP3_Moderate
The computational predictor REVEL gives a score of 0.896 which is above the threshold of 0.773, evidence that correlates with impact to IDUA function at the moderate level based on the specifications of the ClinGen Lysosomal Diseases VCEP (PMID: 36413997) (PP3_Moderate). SpliceAI predicts that the variant has no impact on splicing.
PM2_Supporting
The highest population minor allele frequency in gnomAD v4.1.0 is 0.0001673 (1/5976 alleles) in the Middle Eastern population, which is lower than the ClinGen Lysosomal Diseases VCEP’s threshold for PM2_Supporting (<0.00025), meeting this criterion (PM2_Supporting).
PS3_Supporting
When expressed in COS cells, the activity of the variant was indistinguishable from that of untransfected COS cells (PMID: 11735025) (PS3_Supporting).

Curation History
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