IDS p.Pro425fs
c.1274_1277del · VCV3256012
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
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 | escapes | premature termination codon in the last exon (9 of 9) — the truncated protein is likely expressed. PVS1 input, not an applied code |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -0.76 | GERP -2, phastCons 0.007 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- IDS
- Protein
- p.Pro425fs
- Coding
- c.1274_1277del
- MANE Select
- NM_000202
- Type
- Deletion
- Location
- chrX:149483122 (GRCh38)
- Structure
- AlphaFold pLDDT 93.39 · 2 PDB
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.Pro425= Likely benign ★ 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-pro425fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown