ARSL

protein-coding

arylsulfatase 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]

Previous symbols:
  • CDPX
  • CDPX1
  • ARSE

MANE transcript

NM_000047.3

Inheritance

XL

ClinVar variants

P:52U:165B:186

Top phenotype

Chondrodysplasia punctata 1, X-linked recessive

gnomAD constraint

pLI —, LoF o/e 0.19

Max pathogenic AF

—

Genomic locus

chrX:2,934,045-2,968,475

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~34.4 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

X-linked chondrodysplasia punctata 1STRONG

Inheritance Pattern: XL

Disease ID:MONDO:0010555

Submitter: PanelApp Australia

X-linked chondrodysplasia punctata 1STRONG

Inheritance Pattern: XL

Disease ID:MONDO:0010555

Submitter: Labcorp Genetics (formerly Invitae)

X-linked chondrodysplasia punctata 1SUPPORTIVE

Inheritance Pattern: XL

Disease ID:MONDO:0010555

Submitter: Orphanet

X-linked chondrodysplasia punctata 1DEFINITIVE

Inheritance Pattern: XL

Disease ID:MONDO:0010555

Submitter: G2P

X-linked chondrodysplasia punctata 1DEFINITIVE

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)

Chondrodysplasia punctata 1, X-linked recessiveXL

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

Refs: 7720070; 9863597; 12567415; 18348268; 20301713; 20523025; 23462608; 23470839Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ARSL variants in ClinVar

13 Conditions Cataloged
Chondrodysplasia punctata, brachytelephalangic, autosomalTotal: 309
not providedTotal: 114
X-linked chondrodysplasia punctata 1Total: 63
Inborn genetic diseasesTotal: 52
not specifiedTotal: 40
ARSL-related disorderTotal: 13
Connective tissue disorderTotal: 12
ARSE-related disordersTotal: 5

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.

EffectPLPVUSLBBSum
synonymous
12
clinvar
139
clinvar
8
clinvar
159
missense
7
clinvar
21
clinvar
131
clinvar
32
clinvar
7
clinvar
198
nonsense
6
clinvar
5
clinvar
3
clinvar
14
start loss
0
frameshift
5
clinvar
2
clinvar
1
clinvar
8
splice donor/acceptor (+/-2bp)
6
clinvar
18
clinvar
24
Total183416517115403

Highest pathogenic variant AF is 0.00015554365

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 66 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_000047.3RefSeqNP_000038.210MANE Select
ENST00000381134.9EnsemblENSP00000370526.310MANE Select
NM_001282628.2RefSeqNP_001269557.110Standard
NM_001282631.2RefSeqNP_001269560.29Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense1.951732620.6600.00002233844
Missense (PolyPhen)551170.470081690
Synonymous0.6121101180.9290.00001171191
Loss of Function2.98315.80.1900.00000122234

Population LoF Frequency

PopulationCAFp-valueStatus
African0.0000760.000062rare
Latino/Admixed American00.0absent
Ashkenazi Jewish00.0absent
East Asian0.0000720.000054rare
Finnish00.0absent
European (Non-Finnish)0.0000370.000026rare
South Asian00.0absent
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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