Evidence Repository - Clinical Genome Resources

The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

Variant: NM_000203.5(IDUA):c.1230C>G (p.Thr410=)

Curation Version - 1.3
Curation History
JSON LD for Version 1.3

CA145870

92628 (ClinVar)

Gene: IDUA

Condition: mucopolysaccharidosis type 1

Inheritance Mode: Autosomal recessive inheritance

Link to MONDO

UUID: 94e785cf-ffa3-42ac-b66b-c16a5572b621

Approved on: 2025-01-02

Published on: 2025-03-25

HGVS expressions

NM_000203.5:c.1230C>G

NM_000203.5(IDUA):c.1230C>G (p.Thr410=)

NC_000004.12:g.1002772C>G

CM000666.2:g.1002772C>G

NC_000004.11:g.996560C>G

CM000666.1:g.996560C>G

NC_000004.10:g.986560C>G

NG_008103.1:g.20776C>G

ENST00000247933.9:c.1230C>G

ENST00000514224.2:c.1230C>G

ENST00000652070.1:n.1286C>G

ENST00000247933.8:c.1230C>G

ENST00000502829.1:n.32C>G

ENST00000514224.1:c.834C>G

ENST00000514698.5:n.1337C>G

NM_000203.4:c.1230C>G

NR_110313.1:n.1318C>G

NM_001363576.1:c.834C>G

Benign

BA1

Evidence Links 0

Expert Panel

Lysosomal Diseases VCEP

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.1230C>G variant in IDUA is a synonymous (silent) variant (p.Thr410=). The Grpmax Filtering AF (95% confidence) in gnomAD v4.1.0 is 0.2954 in the South Asian population, which is higher than the ClinGen Lysosomal Diseases VCEP’s threshold for BA1 (>0.005), and therefore meets this criterion (BA1). There is a ClinVar entry for this variant (Variation ID: 92628). In summary, this variant meets the criteria to be classified as benign for mucopolysaccharidosis type 1. IDUA-specific ACMG/AMP criteria applied, as specified by the ClinGen Lysosomal Diseases Variant Curation Expert Panel (Specifications Version 1.0.0): BA1. (Classification approved by the ClinGen Lysosomal Diseases Variant Curation Expert Panel on January 2, 2025)

BA1

The Grpmax Filtering AF (95% confidence) in gnomAD v4.1.0 is 0.2954 in the South Asian population, which is higher than the ClinGen Lysosomal Diseases VCEP’s threshold for BA1 (>0.005), and therefore meets this criterion (BA1). Note: gnomAD v4.1.0. notes "discrepant frequencies" between exomes and genomes. GrpMax is 0.2951 in exomes, 0.2884 in genomes, and 0.2954 overall, all in South Asian and all meeting the BA1 threshold.

Curation History

The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. If you have questions about the information contained on this website, please see a health care professional.