ARSL
protein-codingarylsulfatase L, the group of Sulfatases
Gene summary
Arylsulfatase E is a member of the sulfatase family. It is glycosylated postranslationally and localized to the golgi apparatus. Sulfatases are essential for the correct composition of bone and cartilage matrix. X-linked chondrodysplasia punctata, a disease characterized by abnormalities in cartilage and bone development, has been linked to mutations in this gene. Alternative splicing results in multiple transcript variants. A pseudogene related to this gene is located on the Y chromosome. [provided by RefSeq, Sep 2013]
- CDPX
- CDPX1
- ARSE
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~34.4 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: XL
Disease ID:MONDO:0010555
Submitter: PanelApp Australia
Inheritance Pattern: XL
Disease ID:MONDO:0010555
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: XL
Disease ID:MONDO:0010555
Submitter: Orphanet
Inheritance Pattern: XL
Disease ID:MONDO:0010555
Submitter: G2P
Inheritance Pattern: XL
Disease ID:MONDO:0010555
Submitter: ClinGen
ARSL was first reported in relation to X-linked chondrodysplasia punctata (CDPX), a rare disorder affecting bone and cartilage, in 1976 (Sheffield et al., 1976 PMID 993917) . At least 40 unique variants (missense, nonsense, small deletions) have been reported in humans. Evidence supporting this gene-disease relationship includes case-level and experimental data. Variants in this gene have been reported in at least 50 probands in seven publications. Variants were found to be maternally inherited in all of the cases where mothers of male probands were tested. There was also evidence of segregation in at least three families, where the variant was identified in other family members with similar features (Sheffield et al. 1998 PMID 9863597; Nino et al., 2008 PMID 18348268; Garnier et al., 2007 PMID 16937129). More evidence is available in the literature, but the maximum score for genetic evidence (12 pts) has been reached. The mechanism for CDPX1 is haploinsufficiency. This gene-disease relationship is supported by relevant experimental evidence showing that the biochemical function of ARSL deficiency resulting in CPDX is similar to the phenotype of warfarin embryopathy (Franco et al., 1995 PMID 7720070). Functional alteration resulting in deficiency of heat-labile arylsulfastase activity was shown in CPDX patient cells (Franco et al., 1995 PMID 7720070). In summary, ARSL is definitively associated with X-linked chondrodysplasia punctata. This has been repeatedly demonstrated in both the research and clinical diagnostic settings, and has been upheld over time. This classification was approved by the ClinGen Syndromic Disorders GCEP on 7.28.2020 (SOP Version 7). From the Prenatal GCEP's secondary review on August 29th, 2023: In addition to the previous primary curation, there is also clear prenatal/neonatal phenotype associated with ARSL and X-Linked Chondrodysplasia Punctata, evident in many probands demonstrating the gene-disease association, and biochemical function and functional alteration of patient cells evidence. Common ultrasound findings include polyhydramnios, nasal hypoplasia, and calcification or stippling of bones, while radiograph findings include vertebral calcifications.
Clinical Genomic Database (CGD)
Manifestation: Craniofacial; Musculoskeletal; Neurologic
Intervention: Musculoskeletal
Rationale: Individuals may demonstrate cervical spine stenosis and/or instability, and surveillance may be beneficial to detect and treat (eg, with placement of a cervical collar or spinal fusion) spinal sequelae
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to ARSL variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_000047.3. 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 | 12 | 139 | 8 | 159 | ||
| missense | 7 | 21 | 131 | 32 | 7 | 198 |
| nonsense | 6 | 5 | 3 | 14 | ||
| start loss | 0 | |||||
| frameshift | 5 | 2 | 1 | 8 | ||
| splice donor/acceptor (+/-2bp) | 6 | 18 | 24 | |||
| Total | 18 | 34 | 165 | 171 | 15 | 403 |
Highest pathogenic variant AF is 0.00015554365
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_000038.2 | 10 | MANE Select | |
| Ensembl | ENSP00000370526.3 | 10 | MANE Select | |
| RefSeq | NP_001269557.1 | 10 | Standard | |
| RefSeq | NP_001269560.2 | 9 | 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
Biological Process
- skeletal system development
Molecular Function
- arylsulfatase activity
- metal ion binding
Cellular Component
- endoplasmic reticulum lumen
- Golgi apparatus
- Golgi stack
- extracellular exosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000381134
- Coding exons
- 10
- Length
- 33588
- Individuals with no LoFs
- 125742
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 4
- Defined
- 125747
- p
- 0.0000199
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.95 | 173 | 262 | 0.660 | 0.0000223 | 3844 |
| Missense (PolyPhen) | 55 | 117 | 0.47008 | 1690 | ||
| Synonymous | 0.612 | 110 | 118 | 0.929 | 0.0000117 | 1191 |
| Loss of Function | 2.98 | 3 | 15.8 | 0.190 | 0.00000122 | 234 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000076 | 0.000062 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000072 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000037 | 0.000026 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May be essential for the correct composition of cartilage and bone matrix during development. Has no activity toward steroid sulfates.;
- Disease
- DISEASE: Chondrodysplasia punctata 1, X-linked recessive (CDPX1) [MIM:302950]: A clinically and genetically heterogeneous disorder characterized by punctiform calcification of the bones. CDPX1 is a congenital defect of bone and cartilage development characterized by aberrant bone mineralization, severe underdevelopment of nasal cartilage, and distal phalangeal hypoplasia. This disease can also be induced by inhibition with the drug warfarin. {ECO:0000269|PubMed:12567415, ECO:0000269|PubMed:7720070, ECO:0000269|PubMed:9409863}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.0978
Intolerance Scores
- LoFtool
- 0.124
- RVIS EVS
- 0.29
- RVIS percentile EVS
- 71.51
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.974
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |