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.64C>T (p.Pro22Ser)

CA355945380

553029 (ClinVar)

Gene: IDUA (HGNC:3425)
Condition: mucopolysaccharidosis type 1 (MONDO:0001586)
Inheritance Mode: Autosomal recessive inheritance
UUID: b54443f4-7836-4921-9239-5f59afbaffde
Approved on: 2026-01-05
Published on: 2026-02-05

HGVS expressions

NM_000203.5(IDUA):c.64C>T (p.Pro22Ser)
NM_000203.5:c.64C>T
NC_000004.12:g.987148C>T
CM000666.2:g.987148C>T
NC_000004.11:g.980936C>T
CM000666.1:g.980936C>T
NC_000004.10:g.970936C>T
NG_008103.1:g.5152C>T
NG_033042.1:g.11289G>A
ENST00000247933.9:c.64C>T
ENST00000514224.2:c.64C>T
ENST00000247933.8:c.64C>T
ENST00000398520.6:c.576+3980G>A
ENST00000502910.5:c.64C>T
ENST00000504568.5:c.62C>T
ENST00000506561.5:n.73C>T
ENST00000508168.5:n.83C>T
ENST00000514698.5:n.105C>T
ENST00000622731.4:c.576+3980G>A
NM_000203.4:c.64C>T
NM_134425.2:c.576+3980G>A
NR_110313.1:n.152C>T
NM_134425.3:c.576+3980G>A
NM_134425.4:c.576+3980G>A
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Uncertain Significance

Met criteria codes 3
PP4 PP3 PM2_Supporting
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 1.2.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Lysosomal Diseases VCEP
The NM_000203.5:c.64C>T variant in IDUA is a missense variant predicted to cause substitution of proline by serine at amino acid 22 (p.Pro22Ser). At least one patient with this variant found to be compound heterozygous in documented IDUA deficiency within the affected range in leukocytes [α-Iduronidase enzyme activity 0.01 nmol/21 h*punch] and clinical features specific to MPS I including coarse facial features, hepatosplenomegaly, corneal clouding, gibbus, developmental delay, short stature, frequent respiratory illness and/or umbilical hernia (PP4). One patient compound heterozygous for c.64C>T (p.Pro22Ser) and another variant that has not yet bee classified as pathogenic or likely pathogenic by the ClinGen LD VCEP, c.1829-1G>A; phase unknown (PM3 is not met). The highest population minor allele frequency in gnomAD v4.0. is 9.167e-7 (1/1090820 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). The computational predictor REVEL gives a score of 0.692 which is in the range 0.644-0.773, evidence that correlates with impact to IDUA function at the supporting level (PP3; PMID: 36413997). There is a ClinVar entry for this variant (Variation ID: 553029). In summary, this variant meets the criteria to be classified as variant of uncertain significance 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 1.2.0): PP4, PP3, PM2_Supporting (Classification approved by the ClinGen Lysosomal Diseases Variant Curation Expert Panel on January 5, 2026)
Met criteria codes
PP4
One individua with this variant has been reported with clinical symptoms consistent with MPS I and IDUA activity in the affected range in dried blood spots (PMID:24798265) (PP4).
PP3
The computational predictor REVEL gives a score of 0.692 which is in the range 0.644-0.773, evidence that correlates with impact to IDUA function at the supporting level (PMID: 36413997) (PP3).
PM2_Supporting
The highest population minor allele frequency in gnomAD v4.0. is 9.167e-7 (1/1090820 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
PM3
One patient compound heterozygous for c.64C>T (p.Pro22Ser) and another variant that has not yet bee classified as pathogenic or likely pathogenic by the ClinGen LD VCEP, c.1829-1G>A; phase unknown. (PM3 is not met).
Curation History
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