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 (Definitive), mode of inheritance: XLR
- mucopolysaccharidosis type 2 (Strong), mode of inheritance: AR
- 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 (127 variants)
- not provided (21 variants)
- Inborn genetic diseases (5 variants)
- Mucopolysaccharidosis, MPS-III-A (1 variants)
- Mucopolysaccharidosis type 2, severe form (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.
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.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 185 | 15 | 203 | |||
| missense | 35 | 56 | 127 | 41 | 13 | 272 |
| nonsense | 32 | 37 | ||||
| start loss | 1 | |||||
| frameshift | 43 | 14 | 57 | |||
| inframe indel | 7 | |||||
| splice donor/acceptor (+/-2bp) | 26 | 30 | ||||
| splice region | 2 | 2 | 7 | 24 | 2 | 37 |
| non coding | 68 | 21 | 91 | |||
| Total | 139 | 83 | 133 | 294 | 49 |
Highest pathogenic variant AF is 0.00000897
Variants in IDS
This is a list of pathogenic ClinVar variants found in the IDS region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| X-149482521-TA-T | Benign (Aug 22, 2019) | |||
| X-149482521-T-TA | Likely benign (Aug 13, 2019) | |||
| X-149482745-C-G | IDS-related disorder | Likely benign (May 18, 2020) | ||
| X-149482750-G-C | Mucopolysaccharidosis, MPS-II | Uncertain significance (Jul 02, 2021) | ||
| X-149482750-G-T | Mucopolysaccharidosis, MPS-II | Uncertain significance (Mar 13, 2022) | ||
| X-149482756-A-T | not specified | Uncertain significance (May 15, 2023) | ||
| X-149482757-A-G | Mucopolysaccharidosis, MPS-II • Mucopolysaccharidosis, MPS-III-A | Likely benign (Nov 17, 2023) | ||
| X-149482765-A-G | Uncertain significance (Aug 05, 2024) | |||
| X-149482769-G-T | Mucopolysaccharidosis, MPS-II | Uncertain significance (Jul 25, 2023) | ||
| X-149482770-A-G | Mucopolysaccharidosis, MPS-II | Likely benign (Apr 17, 2022) | ||
| X-149482773-T-G | Mucopolysaccharidosis, MPS-II | Likely benign (Apr 28, 2022) | ||
| X-149482776-A-C | Mucopolysaccharidosis, MPS-II | Likely benign (Nov 13, 2023) | ||
| X-149482778-C-A | Mucopolysaccharidosis, MPS-II | Uncertain significance (Jun 28, 2023) | ||
| X-149482782-G-A | Mucopolysaccharidosis, MPS-II | Likely benign (Apr 13, 2021) | ||
| X-149482787-CA-C | Mucopolysaccharidosis, MPS-II | Pathogenic (Jun 07, 2024) | ||
| X-149482789-T-C | Mucopolysaccharidosis, MPS-II | Uncertain significance (Jan 11, 2022) | ||
| X-149482791-A-G | Mucopolysaccharidosis, MPS-II • IDS-related disorder | Likely benign (Jan 08, 2023) | ||
| X-149482791-A-T | Mucopolysaccharidosis, MPS-II | Likely pathogenic (Jun 07, 2024) | ||
| X-149482798-T-A | Mucopolysaccharidosis, MPS-II | Likely pathogenic (Jun 07, 2024) | ||
| X-149482799-T-G | Mucopolysaccharidosis, MPS-II | Likely pathogenic (Jun 07, 2024) | ||
| X-149482801-T-A | Inborn genetic diseases | Uncertain significance (Dec 28, 2022) | ||
| X-149482808-G-A | Mucopolysaccharidosis, MPS-II | Pathogenic/Likely pathogenic (Jun 07, 2024) | ||
| X-149482809-C-CA | Mucopolysaccharidosis, MPS-II | Pathogenic (Jun 07, 2024) | ||
| X-149482810-A-T | Mucopolysaccharidosis, MPS-II | Pathogenic (Oct 13, 2021) | ||
| X-149482811-A-G | Mucopolysaccharidosis, MPS-II | Likely benign (Jun 01, 2022) |
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 |
|---|---|---|---|---|---|---|
| 0.996 | 0.00360 | 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
Haploinsufficiency Scores
- pHI
- 0.216
- hipred
- Y
- hipred_score
- 0.534
- ghis
- 0.527
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 |
Mouse Genome Informatics
- Gene name
- Ids
- Phenotype
- cellular phenotype; homeostasis/metabolism phenotype; muscle phenotype; craniofacial phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; endocrine/exocrine gland phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; respiratory system phenotype; immune system phenotype; skeleton phenotype; renal/urinary system phenotype; limbs/digits/tail phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; hematopoietic system phenotype;
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