Mucopolysaccharidosis, MPS-II: genes and variants
Mucopolysaccharidosis, MPS-II is linked to 1 analyzed protein (IDS). 193 DNA variants are known to cause it; 139 more are uncertain, and 15 of those already look disease-causing on computable evidence.
Last updated 2026-09-30. Research information, not medical advice.
Genes linked to Mucopolysaccharidosis, MPS-II
IDS: Iduronate 2-sulfatase
It removes sulfate groups from iduronate-containing glycosaminoglycans during lysosomal degradation. Loss-of-function variants cause X-linked Hunter syndrome, with progressive accumulation of dermatan and heparan sulfate affecting multiple organs and, in severe disease, the nervous system.
193 disease-causing and 139 uncertain variants in IDS are linked to Mucopolysaccharidosis, MPS-II.
Known disease-causing variants in Mucopolysaccharidosis, MPS-II
| Variant | Position | Protein part | Clinical label |
|---|---|---|---|
| IDS D46Y | 46 | Disease-causing (★★) | |
| IDS P86R | 86 | Disease-causing (★★) | |
| IDS S152N | 152 | Disease-causing (★★) | |
| IDS S152R | 152 | Disease-causing (★★) | |
| IDS P160H | 160 | Disease-causing (★★) | |
| IDS A205T | 205 | Disease-causing (★★) | |
| IDS H342R | 342 | Disease-causing (★★) | |
| IDS R468Q | 468 | Disease-causing (★★) | |
| IDS P480L | 480 | Disease-causing (★★) | |
| IDS S71I | 71 | Disease-causing (★★) | |
| IDS S71N | 71 | Disease-causing (★★) | |
| IDS A85T | 85 | Disease-causing (★★) | |
| IDS P86L | 86 | Disease-causing (★★) | |
| IDS R88H | 88 | Disease-causing (★★) | |
| IDS R88C | 88 | Disease-causing (★★) | |
| IDS G134E | 134 | Disease-causing (★★) | |
| IDS K135E | 135 | Disease-causing (★★) | |
| IDS K135R | 135 | Disease-causing (★★) | |
| IDS P228L | 228 | Disease-causing (★★) | |
| IDS H229R | 229 | Disease-causing (★★) | |
| IDS P231L | 231 | Disease-causing (★★) | |
| IDS P231R | 231 | Disease-causing (★★) | |
| IDS N265K | 265 | Disease-causing (★★) | |
| IDS D308G | 308 | Disease-causing (★★) | |
| IDS S333L | 333 | Disease-causing (★★) | |
| IDS S333W | 333 | Disease-causing (★★) | |
| IDS D334G | 334 | Disease-causing (★★) | |
| IDS H335Y | 335 | Disease-causing (★★) | |
| IDS G340R | 340 | Disease-causing (★★) | |
| IDS H342P | 342 | Disease-causing (★★) | |
| IDS K347R | 347 | Disease-causing (★★) | |
| IDS S349R | 349 | Disease-causing (★★) | |
| IDS C422R | 422 | Disease-causing (★★) | |
| IDS C422F | 422 | Disease-causing (★★) | |
| IDS C422Y | 422 | Disease-causing (★★) | |
| IDS P467R | 467 | Disease-causing (★★) | |
| IDS R468W | 468 | Disease-causing (★★) | |
| IDS R468P | 468 | Disease-causing (★★) | |
| IDS P469L | 469 | Disease-causing (★★) | |
| IDS P469R | 469 | Disease-causing (★★) | |
| IDS I485K | 485 | Disease-causing (★★) | |
| IDS W502G | 502 | Disease-causing (★★) | |
| IDS E521K | 521 | Disease-causing (★★) | |
| IDS D45G | 45 | Disease-causing (★★) | |
| IDS S71R | 71 | Disease-causing (★★) | |
| IDS A82V | 82 | Disease-causing (★★) | |
| IDS A85S | 85 | Disease-causing (★★) | |
| IDS R95G | 95 | Disease-causing (★★) | |
| IDS Y108C | 108 | Disease-causing (★★) | |
| IDS Y108D | 108 | Disease-causing (★★) | |
| IDS H138R | 138 | Disease-causing (★★) | |
| IDS C184F | 184 | Disease-causing (★★) | |
| IDS G224A | 224 | Disease-causing (★★) | |
| IDS G224E | 224 | Disease-causing (★★) | |
| IDS H229Y | 229 | Disease-causing (★★) | |
| IDS N265I | 265 | Disease-causing (★★) | |
| IDS H335R | 335 | Disease-causing (★★) | |
| IDS G336E | 336 | Disease-causing (★★) | |
| IDS G340D | 340 | Disease-causing (★★) | |
| IDS H342Y | 342 | Disease-causing (★★) |
Showing 60 of 193.
Uncertain variants in Mucopolysaccharidosis, MPS-II that look disease-causing
| Variant | Position | Protein part | Clinical label | Evidence |
|---|---|---|---|---|
| IDS R493C | 493 | Conflicting reports (★) | +7: 3 other pathogenic changes within 3 positions; R493P at the same position is pathogenic; seen in 8.9e-06 of gnomAD DNA copies; REVEL 0.973 | |
| IDS R493H | 493 | Conflicting reports (★) | +7: 3 other pathogenic changes within 3 positions; R493P at the same position is pathogenic; seen in 9.1e-06 of gnomAD DNA copies; REVEL 0.939 | |
| IDS I485T | 485 | Conflicting reports (★) | +7: 3 other pathogenic changes within 3 positions; I485K at the same position is pathogenic; seen in 1.8e-06 of gnomAD DNA copies; REVEL 0.935 | |
| IDS P358T | 358 | Uncertain (★★) | +7: in a 3D region that tolerates change poorly (1R); P358R at the same position is pathogenic; seen in 9.1e-07 of gnomAD DNA copies; REVEL 0.973 | |
| IDS R48H | 48 | Uncertain (★) | +7: 6 other pathogenic changes within 3 positions; R48P at the same position is pathogenic; seen in 9.1e-07 of gnomAD DNA copies; REVEL 0.963 | |
| IDS Y225C | 225 | Uncertain (★★) | +7: 8 other pathogenic changes within 3 positions; Y225D at the same position is pathogenic; seen in 2.7e-06 of gnomAD DNA copies; REVEL 0.920 | |
| IDS Y264C | 264 | Uncertain (★) | +7: 6 other pathogenic changes within 3 positions; Y264N at the same position is pathogenic; seen in 9.1e-07 of gnomAD DNA copies; REVEL 0.920 | |
| IDS P480S | 480 | Uncertain (★★) | +7: 4 other pathogenic changes within 3 positions; P480L at the same position is pathogenic; seen in 1.8e-06 of gnomAD DNA copies; REVEL 0.816 | |
| IDS T118S | 118 | Uncertain (★★) | +7: 6 other pathogenic changes within 3 positions; T118I at the same position is pathogenic; seen in 9e-06 of gnomAD DNA copies; REVEL 0.848 | |
| IDS S349N | 349 | Conflicting reports (★) | +6: 9 other pathogenic changes within 3 positions; S349R at the same position is pathogenic; not seen in the gnomAD population database; AlphaMissense 0.72 | |
| IDS W502R | 502 | Uncertain (★) | +6: 4 other pathogenic changes within 3 positions; W502G at the same position is pathogenic; not seen in the gnomAD population database; AlphaMissense 0.95 | |
| IDS G340S | 340 | Uncertain (★) | +6: 10 other pathogenic changes within 3 positions; G340R at the same position is pathogenic; not seen in the gnomAD population database; AlphaMissense 0.96 | |
| IDS D269G | 269 | Uncertain (★) | +6: 5 other pathogenic changes within 3 positions; D269V at the same position is pathogenic; not seen in the gnomAD population database; AlphaMissense 0.91 | |
| IDS P473S | 473 | Uncertain (★★) | +6: 2 other pathogenic changes within 3 positions; P473L at the same position is pathogenic; seen in 2.7e-06 of gnomAD DNA copies; REVEL 0.763 | |
| IDS A79V | 79 | Uncertain (★★) | +6: 5 other pathogenic changes within 3 positions; A79E at the same position is pathogenic; seen in 6.4e-06 of gnomAD DNA copies; REVEL 0.687 |
Which prediction tools work for Mucopolysaccharidosis, MPS-II
How often each tool ranks a disease-causing variant above a harmless one (AUROC × 100).
- CATVariant: 96 out of 100 (learned from overlapping clinical labels, so this is optimistic)
- PolyPhen-2: 94 out of 100 (learned from overlapping clinical labels, so this is optimistic)
- SIFT: 87 out of 100
- REVEL: 82 out of 100 (learned from overlapping clinical labels, so this is optimistic)
- CADD: 78 out of 100
- phyloP: 75 out of 100
Diseases related to Mucopolysaccharidosis, MPS-II
- Mucopolysaccharidosis, also linked to IDS
- Mucopolysaccharidosis, MPS-III-A, also linked to IDS
Frequently asked questions
Which genes are linked to Mucopolysaccharidosis, MPS-II?
In CATVariant, Mucopolysaccharidosis, MPS-II is linked to 1 analyzed protein: IDS (Iduronate 2-sulfatase).
How many genetic variants are linked to Mucopolysaccharidosis, MPS-II?
376 variants: 193 are classified as disease-causing (pathogenic or likely pathogenic) in ClinVar and 139 are of uncertain significance or have conflicting reports.
Which uncertain variants in Mucopolysaccharidosis, MPS-II look disease-causing?
15 uncertain variants reach the likely-pathogenic range of the ACMG/AMP points scale on computable evidence, for example IDS R493C, IDS R493H, IDS I485T, IDS P358T and IDS R48H. These are leads for expert review, not diagnoses.
Which variant effect predictor works best for Mucopolysaccharidosis, MPS-II?
Among tools not trained on clinical labels, SIFT separates this disease's known disease-causing variants from harmless ones best (AUROC 0.87, based on 99 disease-causing and 46 harmless variants).
About this data
Variant–disease links come from ClinVar, Open Targets and UniProt, pooled from the latest public CATVariant analysis of each human protein. Evidence scores use the ACMG/AMP Bayesian points scale with computable criteria only (position among known disease variants, rarity in gnomAD, calibrated predictors, deep mutational scanning); there is no family or patient data, so they prioritise variants for expert review and never classify them.
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