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
  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_000203.5(IDUA):c.1799del (p.Pro599_Ser600insTer)

CA220505

92636 (ClinVar)

Gene: IDUA
Condition: mucopolysaccharidosis type 1
Inheritance Mode: Autosomal recessive inheritance
UUID: 5fbee9bb-f5a5-4255-9cec-7535f766613f
Approved on: 2024-12-06
Published on: 2024-12-15

HGVS expressions

NM_000203.5:c.1799delC
NM_000203.5:c.1799del
NM_000203.5(IDUA):c.1799del (p.Pro599_Ser600insTer)
NC_000004.12:g.1004083del
CM000666.2:g.1004083del
NC_000004.11:g.997871del
CM000666.1:g.997871del
NC_000004.10:g.987871del
NG_008103.1:g.22087del
ENST00000247933.9:c.1799del
ENST00000514224.2:c.1799del
ENST00000652070.1:n.1855del
ENST00000247933.8:c.1799del
ENST00000514224.1:c.1403del
ENST00000514698.5:n.1910del
NM_000203.4:c.1799del
NR_110313.1:n.1891del
NM_001363576.1:c.1403del
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Likely Pathogenic

Met criteria codes 4
PVS1_Moderate PM3_Strong PM2_Supporting PP4
Not Met criteria codes 2
BS3 PS3

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(IDUA):c.1799del (p.Ser600Ter) variant in IDUA is a frameshift variant predicted to cause a premature stop codon in the last 50 nucleotides of the penultimate exon of the gene and therefore to escape nonsense mediated decay. Less than 10% of the protein is predicted to be removed. (PVS1_Moderate). At least 5 patients with this variant have been reported with this variant, four with documented clinical features consistent with MPS 1 and IDUA deficiency within the affected range in leukocytes; two had mildly elevated GAGs, one after receiving HSCT and one was possibly on treatment (clinical laboratory data) (PP4). Three patients were compound heterozygous for the variant and a variant in IDUA that has been classified as pathogenic or likely pathogenic by the ClinGen LD VCEP (c.208C>T (p.Gln70Ter), c.1728-2A>G, and c.1898C>G (p.Ser633Trp)) and none of those were confirmed in trans (clinical diagnostic lab). At least two individuals were homozygous for the variant PMID: 22976768, clinical diagnostic lab) (PM3_Strong). This variant is absent in gnomAD v4.1.0. (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: 92636). In summary, this variant meets the criteria to be classified as likely 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_Moderate, PP4, PM3_Strong, PM2_Supporting. (Classification approved by the ClinGen Lysosomal Diseases Variant Curation Expert Panel on December 6, 2024)
Met criteria codes
PVS1_Moderate
TheNM_000203.5(IDUA):c.1799del (p.Ser600Ter) variant in IDUA is a frameshift variant predicted to cause a premature stop codon in the last 50 nucleotides of the penultimate exon of the gene and therefore to escape nonsense mediated decay. Less than 10% of the protein is predicted to be removed. (PVS1_Moderate).
PM3_Strong
This variant has been detected in at least 5 individuals with MPS I. Of those individuals, 3 were compound heterozygous for the variant and a variant in IDUA that has been classified as pathogenic or likely pathogenic by the ClinGen LD VCEP (c.208C>T (p.Gln70Ter), c.1728-2A>G, and c.1898C>G (p.Ser633Trp)) and none of those were confirmed in trans (1.5 points; clinical diagnostic lab). At least two individuals were homozygous for the variant (0.5 points; PMID: 22976768, clinical diagnostic lab). Total 2.5 points (PM3_Strong).
PM2_Supporting
This variant is absent in gnomAD v4.1.0. (PM2_Supporting).
PP4
At least 4 patients with this variant have been reported with documented clinical features consistent with MPS 1 and IDUA deficiency within the affected range in leukocytes; two had mildly elevated GAGs, one after receiving HSCT and one was possibly on treatment (clinical laboratory data) (PP4).
Not Met criteria codes
BS3
To our knowledge, the results of functional assays have not been reported for this variant.
PS3
To our knowledge, the results of functional assays have not been reported for this variant.
Curation History
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