IDS
iduronate 2-sulfatase, the group of Sulfatases
Basic information
Region (hg38): X:149476988-149521096
Previous symbols: [ "SIDS" ]
Links
Phenotypes
GenCC
Source:
- mucopolysaccharidosis type 2 (Definitive), mode of inheritance: XL
- mucopolysaccharidosis type 2 (Strong), mode of inheritance: XL
- mucopolysaccharidosis type 2, severe form (Supportive), mode of inheritance: XL
- mucopolysaccharidosis type 2, attenuated form (Supportive), mode of inheritance: XL
- mucopolysaccharidosis type 2 (Strong), mode of inheritance: XL
- mucopolysaccharidosis type 2 (Definitive), mode of inheritance: XL
- mucopolysaccharidosis type 2 (Definitive), mode of inheritance: XL
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Mucopolysaccharidosis type II | XL | Biochemical | Enzyme replacement therapy is available and may positively influence biochemical parameters and some outcomes (such as height and endurance), but there is not evidence that the outcome would be positively affected with earlier (genetic) diagnosis, and replacement may not affect neurologic (CNS) manifestations; Awareness of multisystemic involvement, including cardiac manifestations, may allow early and beneficial management of sequelae such as cardiac valvular disease; BMT has been reported | Biochemical; Cardiovascular | 4622960; 1901826; 1906048; 1303211; 8111411; 7581397; 8940265; 9660053; 9762601; 9501270; 9921913; 10399096; 16912578; 17185020; 18038146; 19901005; 19748810; 20301451; 21502868; 23497636; 23537841; 25541100; 28595941 |
ClinVar
This is a list of variants' phenotypes submitted to
- Mucopolysaccharidosis,_MPS-II (1330 variants)
- not_provided (134 variants)
- Inborn_genetic_diseases (93 variants)
- Mucopolysaccharidosis,_MPS-III-A (63 variants)
- not_specified (40 variants)
- IDS-related_disorder (21 variants)
- Mucopolysaccharidosis_type_2,_severe_form (2 variants)
- Mucopolysaccharidosis,_type_II,_mild_form (2 variants)
- History_of_neurodevelopmental_disorder (1 variants)
- Epidermolysis_bullosa_simplex_with_nail_dystrophy (1 variants)
- See_cases (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the IDS gene is commonly pathogenic or not. These statistics are base on transcript: NM_000000202.8. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 4 | 14 | 196 | 13 | 228 |
| missense | 104 | 237 | 226 | 60 | 7 | 634 |
| nonsense | 85 | 11 | 1 | 97 | ||
| start loss | 1 | 1 | 2 | |||
| frameshift | 241 | 48 | 289 | |||
| splice donor/acceptor (+/-2bp) | 47 | 14 | 12 | 73 | ||
| Total | 479 | 315 | 253 | 256 | 20 |
Highest pathogenic variant AF is 0.000008967001
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| IDS | protein_coding | protein_coding | ENST00000340855 | 9 | 56950 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 125740 | 0 | 2 | 125742 | 0.00000795 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.58 | 162 | 229 | 0.706 | 0.0000184 | 3590 |
| Missense in Polyphen | 40 | 91.673 | 0.43633 | 1445 | ||
| Synonymous | -0.214 | 100 | 97.3 | 1.03 | 0.00000831 | 1109 |
| Loss of Function | 3.77 | 0 | 16.6 | 0.00 | 0.00000116 | 275 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000365 | 0.0000365 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000122 | 0.00000879 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Required for the lysosomal degradation of heparan sulfate and dermatan sulfate.;
- Disease
- DISEASE: Mucopolysaccharidosis 2 (MPS2) [MIM:309900]: An X-linked lysosomal storage disease characterized by intracellular accumulation of heparan sulfate and dermatan sulfate and their excretion in urine. Most children with MPS2 have a severe form with early somatic abnormalities including skeletal deformities, hepatosplenomegaly, and progressive cardiopulmonary deterioration. A prominent feature is neurological damage that presents as developmental delay and hyperactivity but progresses to mental retardation and dementia. They die before 15 years of age, usually as a result of obstructive airway disease or cardiac failure. In contrast, those with a mild form of MPS2 may survive into adulthood, with attenuated somatic complications and often without mental retardation. {ECO:0000269|PubMed:10215411, ECO:0000269|PubMed:10220152, ECO:0000269|PubMed:10447264, ECO:0000269|PubMed:10671065, ECO:0000269|PubMed:10838181, ECO:0000269|PubMed:11015461, ECO:0000269|PubMed:11683780, ECO:0000269|PubMed:11731225, ECO:0000269|PubMed:12655569, ECO:0000269|PubMed:12794697, ECO:0000269|PubMed:1284597, ECO:0000269|PubMed:1303211, ECO:0000269|PubMed:16699754, ECO:0000269|PubMed:7581397, ECO:0000269|PubMed:7599640, ECO:0000269|PubMed:7728156, ECO:0000269|PubMed:7866405, ECO:0000269|PubMed:7887413, ECO:0000269|PubMed:7981716, ECO:0000269|PubMed:8281149, ECO:0000269|PubMed:8566953, ECO:0000269|PubMed:8664909, ECO:0000269|PubMed:8830188, ECO:0000269|PubMed:8940265, ECO:0000269|PubMed:9222763, ECO:0000269|PubMed:9266380, ECO:0000269|PubMed:9375851, ECO:0000269|PubMed:9452044, ECO:0000269|PubMed:9501270, ECO:0000269|PubMed:9660053, ECO:0000269|PubMed:9762601, ECO:0000269|PubMed:9875019, ECO:0000269|PubMed:9921913, ECO:0000269|PubMed:9950361}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Lysosome - Homo sapiens (human);Glycosaminoglycan degradation - Homo sapiens (human);Metabolism of carbohydrates;HS-GAG degradation;Heparan sulfate/heparin (HS-GAG) metabolism;CS/DS degradation;Chondroitin sulfate/dermatan sulfate metabolism;Glycosaminoglycan metabolism;Metabolism
(Consensus)
Recessive Scores
- pRec
- 0.254
Intolerance Scores
- loftool
- rvis_EVS
- 0.38
- rvis_percentile_EVS
- 75.51
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.0204
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Zebrafish Information Network
- Gene name
- ids
- Affected structure
- atrioventricular valve
- Phenotype tag
- abnormal
- Phenotype quality
- disorganized
Gene ontology
- Biological process
- glycosaminoglycan catabolic process;chondroitin sulfate catabolic process
- Cellular component
- lysosomal lumen
- Molecular function
- iduronate-2-sulfatase activity;sulfuric ester hydrolase activity;metal ion binding