IDS p.Ser333=
c.999G>A · rs1483244890 · VCV589006
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0267%, eas)
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 -7.3 | GERP -3.2 |
| Overall | ||
| CADD | 0.185 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0267%
East Asian · 9/33,758 alleles
Filtering AF
0.0139%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0103%
Overall
0.00149%
18/1,208,671 alleles · ultra-rare
exomes 16/1,097,101 · genomes 2/111,570 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0267% | 3,751 |
| African / African-American | 0.00877% | 11,399 |
| South Asian | 0.00176% | 56,798 |
| European (non-Finnish) | 0.000335% | 298,074 |
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
- IDS
- Protein
- p.Ser333=
- Coding
- c.999G>A
- MANE Select
- NM_000202
- dbSNP
- rs1483244890
- Type
- single nucleotide variant
- Location
- chrX:149490321 (GRCh38)
- Structure
- AlphaFold pLDDT 93.39 · 2 PDB
- Residue 333
- a UniProt-annotated variant site (in mps2; severe form); a β-strand
Similar variants
- IDS p.Ser333Leu Pathogenic ★★ same residue
- IDS p.Ser333Trp Pathogenic/Likely pathogenic ★★ same residue
- IDS p.Ser333fs Pathogenic ★ same residue
- IDS c.1006+1G>C Pathogenic ★★ same condition
- IDS c.1006+1G>T Pathogenic ★★ same condition
- IDS c.1007-133A>G Likely pathogenic ★★ same condition
- IDS c.1007-1G>A Pathogenic ★★ same condition
- IDS c.1007-2A>C Pathogenic/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/ids-p-ser333 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown