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.208C>T (p.Gln70Ter)

CA204563

11909 (ClinVar)

Gene: IDUA
Condition: mucopolysaccharidosis type 1
Inheritance Mode: Autosomal recessive inheritance
UUID: 82f2cc6b-74c1-47c7-9ca0-1d5148992608
Approved on: 2025-01-02
Published on: 2025-01-02

HGVS expressions

NM_000203.5:c.208C>T
NM_000203.5(IDUA):c.208C>T (p.Gln70Ter)
NC_000004.12:g.987858C>T
CM000666.2:g.987858C>T
NC_000004.11:g.981646C>T
CM000666.1:g.981646C>T
NC_000004.10:g.971646C>T
NG_008103.1:g.5862C>T
NG_033042.1:g.10579G>A
ENST00000247933.9:c.208C>T
ENST00000398516.3:c.*975G>A
ENST00000514224.2:c.208C>T
ENST00000247933.8:c.208C>T
ENST00000361661.6:c.*975G>A
ENST00000398520.6:c.576+3270G>A
ENST00000502910.5:c.158+616C>T
ENST00000504568.5:c.206C>T
ENST00000506561.5:n.217C>T
ENST00000508168.5:n.177+616C>T
ENST00000514698.5:n.199+616C>T
ENST00000622731.4:c.576+3270G>A
NM_000203.4:c.208C>T
NM_022042.3:c.*975G>A
NM_134425.2:c.576+3270G>A
NM_213613.3:c.*975G>A
NR_110313.1:n.296C>T
NM_022042.4:c.*975G>A
NM_134425.3:c.576+3270G>A
NM_213613.4:c.*975G>A
NM_134425.4:c.576+3270G>A
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Pathogenic

Met criteria codes 3
PVS1 PP4 PM3
Not Met criteria codes 2
BS1 PM2

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.208C>T (p.Gln70Ter) variant in IDUA is a nonsense variant predicted to cause a premature stop codon in biologically-relevant-exon 2 of a total of 14 exons, leading to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism. An immunochemical assay performed in fibroblast lines from two individuals homozygous for the variant and three individuals compound heterozygous for the variant and p.Trp402Ter found no detectable IDUA protein (PMID: 1301941) (PVS1). This variant is the second most common variant identified in patients with mucopolysacchararidosis type 1 (MPS1), and is present mainly in Northern Europe, including Norway (54% of MPS1 alleles), Russia (42% of MPS1 alleles), Poland (30% of MPS1 alleles), and Austria (31% of MPS1 alleles) (Reviewed in PMID: 29393969). At least 14 homozygotes (max 0.5 x 2 points = 1 point) and at least 45 individuals who are compound heterozygous for the variant and a second variant in IDUA, including another well-known pathogenic variant, c.1205G>A (p.Trp402Ter) (ClinVar Variation ID: 11908), have been reported (PMID: 1301941, 7951228, 11735025, 28752568). The allelic data for many of these patients will be used in the classification of the second variant and is not included here to avoid circular logic. Therefore, only 1 point was awarded here, the maximum points for homozygotes (PM3). Patients meeting two of the requirements for PP4, IDUA deficiency and elevated urine GAG levels have been reported (PMID: 1301941) (PP4). The highest population minor allele frequency in gnomAD v4.1.0 is 0.002123 in the Finnish population, followed by 0.0005348 in the European non-Finnish population. This is higher than the Lysosomal Diseases VCEP's threshold for PM2_Supporting (<0.00025) and lower than the threshold for BS1 (>0.0025). Therefore, no population codes are met. More data is available in the literature but the classification of pathogenic has already been reached. There is a ClinVar entry for this variant (Variation ID: 11909). In summary, c.208C>T (p.Gln70Ter) is the second most frequent variant identified in patients with MPS1 and meets the criteria to be classified as pathogenic for this condition. IDUA-specific ACMG/AMP criteria met, as specified by the ClinGen Lysosomal Diseases VCEP (Specifications Version 1.0.0): PVS1, PM3, PP4. (Classification approved by the ClinGen Lysosomal Diseases Variant Curation Expert Panel on January 2, 2025)
Met criteria codes
PVS1
The NM_000203.5:c.208C>T (p.Gln70Ter) variant in IDUA is a nonsense variant predicted to cause a premature stop codon in biologically-relevant-exon 2 out of 14 total exons, leading to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism. An immunochemical assay performed in fibroblast lines from two individuals homozygous for the variant and three individuals compound heterozygous for the variant and p.Trp402Ter found no detectable IDUA protein (PMID: 1301941) (PVS1).
PP4
At least 14 homozygotes and at least 45 individuals have been reported in the literature including some patients meeting two of the requirements for PP4, IDUA deficiency and elevated urine GAG levels (PMID: 1301941).
PM3
At least 14 homozygotes (max 0.5 x 2 points = 1 point) and at least 45 individuals who are compound heterozygous for the variant and a second variant in IDUA, including another well-known pathogenic variant, c.1205G>A (p.Trp402Ter) (ClinVar Variation ID: 11908), have been reported (PMID: 1301941, 7951228, 11735025, 28752568). The allelic data for many of these patients will be used in the classification of the second variant and is not included here to avoid circular logic. Therefore, only 1 point was awarded here, the maximum points for homozygotes (PM3).
Not Met criteria codes
BS1
The highest population minor allele frequency in a continental population in gnomAD v2.1.1 is 0.00194 (48/24766 alleles) in the Finnish population. which is lower than the ClinGen LSD VCEP’s threshold for BS1 (>0.0025). Therefore, BS1 is not met.
PM2
The highest population minor allele frequency in gnomAD v4.1.0 is 0.002123 in the Finnish population, followed by 0.0005348 in the European non-Finnish population. This is higher than the Lysosomal Diseases VCEP's threshold for PM2_Supporting (<0.00025) and, therefore, does not meet this criterion.
Curation History
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