IDUA p.Ser586=
c.1758T>C · rs766308077 · VCV1093496
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.0055%, sas)
Conditions
2
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.31 | GERP -3.2 |
| Overall | ||
| CADD | 4.955 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0055%
South Asian · 5/90,930 alleles
Filtering AF
0.00211%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00137%
Overall
0.000342%
5/1,461,366 alleles · very rare
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- IDUA
- Protein
- p.Ser586=
- Coding
- c.1758T>C
- MANE Select
- NM_000203
- dbSNP
- rs766308077
- Type
- single nucleotide variant
- Location
- chr4:1004042 (GRCh38)
- Gene constraint
- LOEUF 1.344 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 95.12 · 11 PDB
- Residue 586
- a β-strand
Similar variants
- IDUA p.Ser586Phe Uncertain significance ★★ ⚠ same residue
- IDUA c.1190-10C>A Likely pathogenic ★★★ same condition
- IDUA c.1190-1G>A Pathogenic ★★★ same condition
- IDUA c.1402+1G>A Likely pathogenic ★★★ same condition
- IDUA c.1402+1G>T Likely pathogenic ★★★ same condition
- IDUA c.1402+2T>G Likely pathogenic ★★★ same condition
- IDUA c.1403-1G>T Pathogenic ★★★ same condition
- IDUA c.1650+1G>T Likely pathogenic ★★★ same condition
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/idua-p-ser586 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown