ARSD
protein-codingarylsulfatase D, the group of Sulfatases
Gene summary
The protein encoded by this gene is a member of the sulfatase family. Sulfatases are essential for the correct composition of bone and cartilage matrix. The encoded protein is postranslationally glycosylated and localized to the lysosome. This gene is located within a cluster of similar arylsulfatase genes on chromosome X. A related pseudogene has been identified in the pseudoautosomal region of chromosome Y. [provided by RefSeq, Jul 2011]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~25.4 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to ARSD variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001669.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 13 | 2 | 1 | 16 | ||
| missense | 109 | 14 | 2 | 125 | ||
| nonsense | 4 | 1 | 5 | |||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 14 | 14 | ||||
| Total | 0 | 0 | 141 | 17 | 3 | 161 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001660.2 | 10 | MANE Select | |
| Ensembl | ENSP00000370546.1 | 10 | MANE Select | |
| RefSeq | NP_033667.2 | 7 | Standard | |
| Ensembl | ENSP00000409180.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Estrogen metabolism
- Metabolism of lipids
- Post-translational protein modification
- Metabolism of proteins
- The activation of arylsulfatases
Molecular Function
- arylsulfatase activity
- metal ion binding
Cellular Component
- lysosome
- endoplasmic reticulum lumen
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000381154
- Coding exons
- 10
- Length
- 25382
- Individuals with no LoFs
- 125687
- Homozygous LoFs
- 13
- Heterozygous LoFs
- 48
- Defined
- 125748
- p
- 0.000243
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.09 | 199 | 247 | 0.805 | 0.0000211 | 3811 |
| Missense (PolyPhen) | 53 | 82.283 | 0.64412 | 1387 | ||
| Synonymous | 0.704 | 109 | 119 | 0.918 | 0.0000121 | 1194 |
| Loss of Function | 1.97 | 7 | 15.3 | 0.457 | 0.00000119 | 251 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.0020 | 0.0015 | notable |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000051 | 0.000035 | rare |
| South Asian | 0.00022 | 0.00013 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.144
Intolerance Scores
- LoFtool
- 0.0885
- RVIS EVS
- 0.18
- RVIS percentile EVS
- 66.07
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |