IDS p.Phe137fs
c.409_412del · VCV3255702
Pathogenic
Multiple submitters
Classification
Pathogenic
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
mucopolysaccharidosis type 2
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | predicted | premature termination codon in exon 3 of 9 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 7.7 | GERP 1.1, phastCons 1 |
| Region caveats | ||
| Repeat context | seg dup | · reads may not map uniquely · confidence, not pathogenicity |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- IDS
- Protein
- p.Phe137fs
- Coding
- c.409_412del
- MANE Select
- NM_000202
- Type
- Deletion
- Location
- chrX:149503318 (GRCh38)
- Structure
- AlphaFold pLDDT 93.39 · 2 PDB
- Residue 137
- a β-strand
Disease context
mucopolysaccharidosis type 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Mucopolysaccharidosis type 2 (Orphanet):
- Inheritance
- X-linked recessive
- Onset
- Childhood
- Prevalence
- 1-9 / 1 000 000 (Europe)
Similar variants
- IDS p.Phe137Ser Pathogenic ★ same residue
- IDS c.418+1_418+4del Pathogenic ★★ same condition
- IDS p.Arg468fs Pathogenic/Likely pathogenic ★★ same condition
- IDS p.Arg8fs Pathogenic ★★ same condition
- IDS p.Arg96del Likely pathogenic ★★ same condition
- IDS p.Asn280fs Pathogenic ★★ same condition
- IDS p.Asp319fs Pathogenic ★★ same condition
- IDS p.Gln474fs 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-phe137fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown