ARSA

gene
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Also known as ASA

Summary

ARSA (arylsulfatase A, HGNC:713) is a protein-coding gene on chromosome 22q13.33, encoding Arylsulfatase A (P15289). Hydrolyzes cerebroside sulfate.

The protein encoded by this gene hydrolyzes cerebroside sulfate to cerebroside and sulfate. Defects in this gene lead to metachromatic leucodystrophy (MLD), a progressive demyelination disease which results in a variety of neurological symptoms and ultimately death. Alternatively spliced transcript variants have been described for this gene.

Source: NCBI Gene 410 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): metachromatic leukodystrophy (Definitive, ClinGen) — +1 more curated relationship
  • GWAS associations: 6
  • Clinical variants (ClinVar): 1,329 total — 164 pathogenic, 134 likely-pathogenic
  • Phenotypes (HPO): 66
  • Druggable target: yes
  • MANE Select transcript: NM_000487

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:713
Approved symbolARSA
Namearylsulfatase A
Location22q13.33
Locus typegene with protein product
StatusApproved
AliasesASA
Ensembl geneENSG00000100299
Ensembl biotypeprotein_coding
OMIM607574
Entrez410

Gene structure

Transcript identifiers

Ensembl transcripts: 17 — 14 protein_coding, 1 retained_intron, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000216124, ENST00000356098, ENST00000395619, ENST00000395621, ENST00000453344, ENST00000551731, ENST00000608497, ENST00000610191, ENST00000861936, ENST00000861937, ENST00000861938, ENST00000861939, ENST00000861940, ENST00000861941, ENST00000861942, ENST00000861943, ENST00000963449

RefSeq mRNA: 6 — MANE Select: NM_000487 NM_000487, NM_001085425, NM_001085426, NM_001085427, NM_001085428, NM_001362782

CCDS: CCDS14100, CCDS46736

Canonical transcript exons

ENST00000216124 — 8 exons

ExonStartEnd
ENSE000006578125062557950625681
ENSE000006578145062593650626063
ENSE000006578165062615450626278
ENSE000006578185062659150626760
ENSE000006578205062683450627052
ENSE000008789595062755650628152
ENSE000035956945062716650627406
ENSE000038457105062275450625464

Expression profiles

Bgee: expression breadth ubiquitous, 177 present calls, max score 95.70.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 17.3543 / max 118.4096, expressed in 1803 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
19480217.35431803

Top tissues by expression

283 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
right uterine tubeUBERON:000130295.70gold quality
right testisUBERON:000453495.49gold quality
granulocyteCL:000009495.43gold quality
mucosa of transverse colonUBERON:000499195.35gold quality
left testisUBERON:000453395.28gold quality
apex of heartUBERON:000209893.68gold quality
adenohypophysisUBERON:000219693.34gold quality
minor salivary glandUBERON:000183093.27gold quality
right lobe of thyroid glandUBERON:000111993.20gold quality
small intestine Peyer’s patchUBERON:000345493.03gold quality
right hemisphere of cerebellumUBERON:001489092.88gold quality
left lobe of thyroid glandUBERON:000112092.79gold quality
transverse colonUBERON:000115792.74gold quality
right lobe of liverUBERON:000111492.70gold quality
body of pancreasUBERON:000115092.56gold quality
body of stomachUBERON:000116192.22gold quality
left coronary arteryUBERON:000162692.22gold quality
descending thoracic aortaUBERON:000234592.02gold quality
C1 segment of cervical spinal cordUBERON:000646991.91gold quality
cerebellar hemisphereUBERON:000224591.90gold quality
ascending aortaUBERON:000149691.86gold quality
lower esophagus mucosaUBERON:003583491.86gold quality
thoracic aortaUBERON:000151591.84gold quality
right adrenal glandUBERON:000123391.75gold quality
spleenUBERON:000210691.69gold quality
right adrenal gland cortexUBERON:003582791.69gold quality
right coronary arteryUBERON:000162591.68gold quality
cerebellar cortexUBERON:000212991.62gold quality
right atrium auricular regionUBERON:000663191.58gold quality
saliva-secreting glandUBERON:000104491.46gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 3.

ExperimentMarker?Max mean expression
E-CURD-122yes39.47
E-ANND-3yes14.61
E-MTAB-10553yes8.78

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

51 targeting ARSA, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-453199.9969.703181
HSA-MIR-150-5P99.9966.691976
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-221-5P99.8665.451052
HSA-MIR-807399.8665.211118
HSA-MIR-674599.7465.331321
HSA-MIR-430699.7270.503630
HSA-MIR-4524A-3P99.7266.852406
HSA-MIR-149-3P99.7268.223963
HSA-MIR-6715B-5P99.6469.631420
HSA-MIR-182799.6368.573265
HSA-MIR-426999.5569.891373
HSA-MIR-363-5P99.4664.511015
HSA-MIR-132499.4666.571302
HSA-MIR-318299.4068.152454
HSA-MIR-103A-1-5P99.3967.781545
HSA-MIR-103A-2-5P99.3967.721577
HSA-MIR-94099.3766.142064
HSA-MIR-185-5P99.3568.602497
HSA-MIR-464499.3569.122514
HSA-MIR-6808-5P99.3166.232150
HSA-MIR-6893-5P99.3166.252119
HSA-MIR-504-3P99.3067.181745
HSA-MIR-485-5P99.1064.781889
HSA-MIR-6884-5P99.1064.501987
HSA-MIR-447899.0765.162320
HSA-MIR-670-3P99.0368.882404

Literature-anchored findings (GeneRIF, showing 40)

  • Multiple alleles in a subject unaffected with metachromatic leucodystrophy (PMID:11333871)
  • contribution of mutations to enzyme activity reduction and metachromatic leukodystrophy severity (PMID:11941485)
  • analysis of arylsulfatase A mutations demonstrates a lack of association with Alzheimer-type dementia or Down syndrome (PMID:12459318)
  • the reduced lysosomal half-life of some mutated forms of ARSA is related to deficient octamerization (PMID:12788103)
  • Structures of human arylsulfatase A crystals soaked in solutions containing 4-methylumbelliferyl phosphate and O-phospho-DL-tyrosine have been determined at 2.7- and 3.2-A resolution, respectively. Phosphate and calcium binding sites are identified. (PMID:12888274)
  • Metachromatic leukodystrophy Molecular analysis revealed compound heterozygosity for two novel missense mutations affecting conserved residues in the arylsulphatase A (ASA) sulphatase and carboxyterminal domains, with 89% loss of enzymatic activity. (PMID:15026521)
  • missense mutation in which actual pathogenic effect was splicing-related by disrupting a potential exonic splicing enhancer (ESE) and causing a complete exon 7 skipping (PMID:15375602)
  • Genetic analysis revealed homozygosity for a novel mutation in exon 3 of ARSA (F219V). (PMID:15710861)
  • Enzyme replacement therapy, using ARSA, improves nervous system pathology and function in a mouse model for metachromatic leukodystrophy. (PMID:15772092)
  • Homozygote for mutation of the ARSA gene presents with a late-infantile form of metachromatic leukodystrophy (PMID:16110195)
  • Adeno-associated virus serotype 5-mediated brain delivery of ARSA is a potentially efficacious therapeutic strategy for metachromatic leukodystrophy patients, especially for those with rapidly progressive form of the disease. (PMID:16311251)
  • Novel mutations in the arylsulfatase A gene in eight Italian families with metachromatic leukodystrophy (PMID:16678723)
  • decidual levels of arylsulphatase A showed very low values at 41 weeks, which reduced to a half at 42 weeks of gestation (PMID:17329011)
  • Six DNA variants of the arylsulfatase A gene were identified: two novel frameshift mutations (c.179_180dupCA and c.1338dupC), one known nonsense mutation (p.W318X), and three known missense mutations (p.R84Q, p.G99V, and p.R288C) (PMID:17560502)
  • Induction of tolerance to human ARSA in a mouse model of metachromatic leukodystrophy is reported. (PMID:17660863)
  • Safety of ARSA overexpression for gene therapy of metachromatic leukodystrophy was evaluated. (PMID:17845130)
  • R95Q, G144R, H393P, & C521Y cause large structural changes, & are associated with the severe phenotype of mucopolysaccharidosis VI. G137V & Y210C are thought to cause small structural changes in a limited region resulting in the attenuated phenotype. (PMID:18248830)
  • 11 novel ARSA alleles in Italian patients with metachromatic leukodystrophy are described. (PMID:18693274)
  • DNA sequencing revealed two novel disease-causing missense mutations in the arylsulfatase gene in patients with metachromatic leukodystrophy (PMID:18768108)
  • the novel Metachromatic leukodystrophy- causing mutations in the exons 2, 5 and even in 8 of the ARSA gene described here can be classified as severe type 0, leading in homozygosity to the late infantile form Metachromatic leukodystrophy (PMID:19021637)
  • We report on two patients with mental retardation, dysmorphic features and low catalytic activity of arylsulfatase A which is because of were explained, in each patients, by a deletion of 22q13 and, thereby, of one allele of ARSA. (PMID:19054018)
  • Saposin B(Sap B) is not a limiting factor of the coupled Sap B-ASA reaction in mouse kidney cells even if sulfatide has accumulated to unphysiologically high levels (PMID:19224915)
  • characterized eight newly identified ARSA mutations, through lentiviral vector-based expression studies on cell lines and ARSA defective murine fibroblasts. The residual activity associated with the new mutant allele correlates well with the phenotype (PMID:19606494)
  • ARSA mutations in the Indian population were characterized. 4 new variant & 5 pseudodeficiency alleles were found. Protein modeling showed loss of interactions leading to conformation change. (PMID:21167507)
  • case report of missense mutations p.G99D and p.T409I associated with adult-type metachromatic leukodystrophy (PMID:21265945)
  • cationization of ASA and an increase of the mannose 6-phosphate content of the enzyme may promote blood-to-brain transfer of ASA, thus leading to an improved therapeutic efficacy of enzyme replacement therapy behind the BBB. (PMID:21454621)
  • The presence of two most common mutations associated with Arylsulfatase A pseudodeficiency was analyzed in 56 patients with diagnosis of relapsing-remitting multiple sclerosis, by polymerase chain reaction restriction fragment length polymorphism method. (PMID:21648305)
  • The purpose was to estimate the birth prevalence of Metachromatic leukodystrophy in Poland by determining population frequency of the common pathogenic ARSA gene mutations and to compare this estimate with epidemiological data. (PMID:21695197)
  • This is the first report that human adipocytes express functional DAR and ARSA, suggesting a regulatory role for peripheral DA in adipose functions. (PMID:21966540)
  • Studied brain uptake in the rhesus monkey of a fusion protein of arylsulfatase a and a monoclonal antibody against the human insulin receptor. (PMID:23192358)
  • The interaction between SPAM1, ARSA and HSPA2 in a multimeric complex mediating sperm-egg interaction. (PMID:23209833)
  • HSPA2 regulates the expression of sperm surface receptors involved in human sperm-oocyte recognition, such as arylsulfatase A and SPAM1. (PMID:23247813)
  • Arylsulphatase A activity in human endometrial polyps inversely correlates with aging (PMID:23689179)
  • Sixteen novel mutations that cause metachromatic leukodystrophy have been identified in the arylsulfatase A gene. (PMID:24001781)
  • We report three families with Arylsulphatase A partial deficit in which we can find a high recurrence of parkinsonism among the siblings. (PMID:24989669)
  • Data indicate a significant correlation between the mutation of c.622delC(p.His208Metfs*46) in the arylsulfatase A (ARSA) gene and the phenotype OF metachromatic leukodystrophy. (PMID:25297594)
  • an extensive review of all the ARSA-causative variants published in the literature to date, accounting for a total of 200 ARSA allele types (review) (PMID:26462614)
  • First report of arylsulfatase A pseudodeficiency (ASA-PD) allele and haplotype frequencies in a North African population, reveals relatively high prevalence of the ASA-PD allele in the Tunisian population with an intermediate genetic structure between Africans, Middle-eastern and Europeans most probably linked to the particular geographic location of Tunisia and the several population incursions throughout its history (PMID:26577183)
  • siblings exhibited compound heterozygous variants {[c.302G>T]+[c.1344dupC]} in the ARSA gene, and both of the variants have been reported as disease-causing mutations previouslyfa (PMID:27374302)
  • The novel p.L113P mutation in a Pakistani family with late infantile MLD has a pathogenic and destructive effect on the protein structure and function of ARSA. (PMID:28799099)

Cross-species orthologs

11 orthologs

OrganismSymbolGene ID
danio_rerioarsaENSDARG00000042270
mus_musculusArsaENSMUSG00000022620
rattus_norvegicusArsaENSRNOG00000012953
drosophila_melanogasterCG18278FBGN0033836
drosophila_melanogasterCG7408FBGN0036765
drosophila_melanogasterCG7402FBGN0036768
drosophila_melanogasterSulf1FBGN0040271
drosophila_melanogasterCG32191FBGN0052191
drosophila_melanogasterCG30059FBGN0260475
caenorhabditis_elegansWBGENE00006308
caenorhabditis_elegansWBGENE00006309

Paralogs (16): ARSD (ENSG00000006756), IDS (ENSG00000010404), ARSF (ENSG00000062096), STS (ENSG00000101846), ARSB (ENSG00000113273), GNS (ENSG00000135677), SULF1 (ENSG00000137573), GALNS (ENSG00000141012), ARSG (ENSG00000141337), ARSL (ENSG00000157399), ARSK (ENSG00000164291), ARSJ (ENSG00000180801), SGSH (ENSG00000181523), ARSI (ENSG00000183876), SULF2 (ENSG00000196562), ARSH (ENSG00000205667)

Protein

Protein identifiers

Arylsulfatase AP15289 (reviewed: P15289)

Alternative names: Cerebroside-sulfatase

All UniProt accessions (3): P15289, A0A0C4DFZ2, V9GYR0

UniProt curated annotations — full annotation on UniProt →

Function. Hydrolyzes cerebroside sulfate.

Subunit / interactions. Homodimer at neutral pH and homooctamer at acidic pH. Exists both as a single chain of 58 kDa (component A) or as a chain of 50 kDa (component B) linked by disulfide bond(s) to a 7 kDa chain (component C). Interacts with SUMF1.

Subcellular location. Endoplasmic reticulum. Lysosome.

Post-translational modifications. The conversion to 3-oxoalanine (also known as C-formylglycine, FGly), of a serine or cysteine residue in prokaryotes and of a cysteine residue in eukaryotes, is critical for catalytic activity. This post-translational modification is severely defective in multiple sulfatase deficiency (MSD).

Disease relevance. Metachromatic leukodystrophy (MLD) [MIM:250100] An autosomal recessive disease caused by abnormal intralysosomal accumulation of cerebroside-3-sulfate in central and peripheral nervous systems, as well as other organs. MLD is clinically characterized by leukodystrophy, progressive demyelination and a variety of neurological symptoms, including gait disturbances, ataxias, optical atrophy, dementia, seizures, and spastic tetraparesis. Decreased arylsulfatase A activity is detected in urine, leukocytes, and fibroblasts of affected individuals. Several forms of the disease can be distinguished according to the age at onset and disease severity: late infantile, juvenile and adult forms, partial cerebroside sulfate deficiency, and pseudoarylsulfatase A deficiency. Individuals with pseudoarylsulfatase A deficiency have low arylsulfatase A activity but lack neurological manifestations and are apparently healthy. The disease is caused by variants affecting the gene represented in this entry. Multiple sulfatase deficiency (MSD) [MIM:272200] A clinically and biochemically heterogeneous disorder caused by the simultaneous impairment of all sulfatases, due to defective post-translational modification and activation. It combines features of individual sulfatase deficiencies such as metachromatic leukodystrophy, mucopolysaccharidosis, chondrodysplasia punctata, hydrocephalus, ichthyosis, neurologic deterioration and developmental delay. The protein represented in this entry is involved in disease pathogenesis. Arylsulfatase A activity is impaired in multiple sulfatase deficiency due to mutations in SUMF1. SUMF1 mutations result in defective post-translational modification of ARSA at residue Cys-69 that is not converted to 3-oxoalanine.

Activity regulation. Inhibited by phosphate. The phosphate forms a covalent bond with the active site 3-oxoalanine.

Cofactor. Binds 1 Ca(2+) ion per subunit.

Miscellaneous. The metal cofactor was first identified as magnesium ion, based on the structure of the recombinant protein, but when purified from human placenta, the protein contains 1 calcium ion per subunit.

Similarity. Belongs to the sulfatase family.

Isoforms (2)

UniProt IDNamesCanonical?
P15289-11yes
P15289-22

RefSeq proteins (6): NP_000478, NP_001078894, NP_001078895, NP_001078896, NP_001078897, NP_001349711 (=MANE)

Domains & families (InterPro)

IDNameType
IPR000917Sulfatase_NDomain
IPR017850Alkaline_phosphatase_core_sfHomologous_superfamily
IPR024607Sulfatase_CSConserved_site
IPR050738SulfataseFamily

Pfam: PF00884, PF14707

Catalyzed reactions (Rhea), 1 shown:

  • an N-acyl-1-beta-D-(3-O-sulfo)-galactosyl-sphing-4-enine + H2O = a beta-D-galactosyl-(1<->1’)-N-acylsphing-4-enine + sulfate + H(+) (RHEA:21300)

UniProt features (187 total): sequence variant 108, strand 21, helix 21, binding site 9, turn 7, disulfide bond 6, chain 3, mutagenesis site 3, glycosylation site 3, active site 2, signal peptide 1, sequence conflict 1, modified residue 1, splice variant 1

Structure

Experimental structures (PDB)

10 structures.

PDBMethodResolution (Å)
2AIJX-RAY DIFFRACTION1.55
2HI8X-RAY DIFFRACTION1.64
2AIKX-RAY DIFFRACTION1.73
1AUKX-RAY DIFFRACTION2.1
1E2SX-RAY DIFFRACTION2.35
1E1ZX-RAY DIFFRACTION2.4
1E33X-RAY DIFFRACTION2.5
1E3CX-RAY DIFFRACTION2.65
1N2KX-RAY DIFFRACTION2.75
1N2LX-RAY DIFFRACTION3.2

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P15289-F196.430.95

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (2): 69 (nucleophile); 125

Ligand- & substrate-binding residues (9): 150; 229; 281; 282; 302; 29; 30; 69 (via 3-oxoalanine); 123

Post-translational modifications (1): 69

Disulfide bonds (6): 156–172, 161–168, 300–414, 488–500, 489–502, 493–499

Glycosylation sites (3): 158, 184, 350

Mutagenesis-validated functional residues (3):

PositionPhenotype
69–70strongly reduces formation of 3-oxoalanine (also known as c-formylglycine, fgly).
69abolishes enzyme activity.
69abolishes formation of 3-oxoalanine (also known as c-formylglycine, fgly). strongly decreases enzyme activity.

Function

Pathways and Gene Ontology

Reactome pathways

12 pathways

IDPathway
R-HSA-1663150The activation of arylsulfatases
R-HSA-6798695Neutrophil degranulation
R-HSA-9840310Glycosphingolipid catabolism
R-HSA-1430728Metabolism
R-HSA-163841Gamma carboxylation, hypusinylation, hydroxylation, and arylsulfatase activation
R-HSA-1660662Glycosphingolipid metabolism
R-HSA-168249Innate Immune System
R-HSA-168256Immune System
R-HSA-392499Metabolism of proteins
R-HSA-428157Sphingolipid metabolism
R-HSA-556833Metabolism of lipids
R-HSA-597592Post-translational protein modification

MSigDB gene sets: 250 (showing top): REACTOME_INNATE_IMMUNE_SYSTEM, GRUETZMANN_PANCREATIC_CANCER_DN, GOCC_SECRETORY_GRANULE, KEGG_LYSOSOME, HOSHIDA_LIVER_CANCER_SUBCLASS_S3, MODULE_256, GOBP_LIPID_METABOLIC_PROCESS, SANSOM_APC_TARGETS_DN, GUO_HEX_TARGETS_UP, MODULE_408, IGLESIAS_E2F_TARGETS_UP, REACTOME_SPHINGOLIPID_METABOLISM, KEGG_SPHINGOLIPID_METABOLISM, GOCC_LYSOSOMAL_LUMEN, GOCC_SECRETORY_VESICLE

GO Biological Process (8): lipid metabolic process (GO:0006629), autophagy (GO:0006914), binding of sperm to zona pellucida (GO:0007339), response to nutrient (GO:0007584), response to pH (GO:0009268), response to estrogen (GO:0043627), response to ethanol (GO:0045471), response to methylmercury (GO:0051597)

GO Molecular Function (7): arylsulfatase activity (GO:0004065), cerebroside-sulfatase activity (GO:0004098), calcium ion binding (GO:0005509), sulfuric ester hydrolase activity (GO:0008484), protein binding (GO:0005515), hydrolase activity (GO:0016787), metal ion binding (GO:0046872)

GO Cellular Component (13): extracellular region (GO:0005576), lysosome (GO:0005764), endoplasmic reticulum lumen (GO:0005788), azurophil granule lumen (GO:0035578), lysosomal lumen (GO:0043202), extracellular exosome (GO:0070062), acrosomal vesicle (GO:0001669), obsolete extracellular space (GO:0005615), endosome (GO:0005768), endoplasmic reticulum (GO:0005783), plasma membrane (GO:0005886), membrane (GO:0016020), extrinsic component of external side of plasma membrane (GO:0031232)

Reactome top-level categories

Rollup of top-9 pathways:

CategoryPathways
Gamma carboxylation, hypusinylation, hydroxylation, and arylsulfatase activation1
Innate Immune System1
Glycosphingolipid metabolism1
Post-translational protein modification1
Sphingolipid metabolism1
Immune System1
Metabolism of lipids1
Metabolism1
Metabolism of proteins1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
response to chemical2
sulfuric ester hydrolase activity2
cellular anatomical structure2
vacuolar lumen2
endomembrane system2
primary metabolic process1
catabolic process1
transmembrane transport1
process utilizing autophagic mechanism1
sperm-egg recognition1
response to nutrient levels1
response to abiotic stimulus1
response to hormone1
response to alcohol1
metal ion binding1
hydrolase activity, acting on ester bonds1
binding1
catalytic activity1
cation binding1
lytic vacuole1
endoplasmic reticulum1
intracellular organelle lumen1
secretory granule lumen1
azurophil granule1
lysosome1
extracellular vesicle1
secretory granule1
cytoplasmic vesicle1
cytoplasm1
intracellular membrane-bounded organelle1
membrane1
cell periphery1
external side of plasma membrane1
extrinsic component of plasma membrane1

Protein interactions and networks

STRING

1166 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ARSAPSAPP07292911
ARSAGALCP54803859
ARSAGUSBP08236838
ARSAASAH1Q13510782
ARSAHPCAP32076781
ARSASUMF1Q8NBK3781
ARSACYB5R3P00387774
ARSAGLAP06280754
ARSAIDUAP35475690
ARSAGLB1P16278689
ARSAGBA1P04062662
ARSASMPD1P17405643
ARSAHSPA2P54652626
ARSASPAM1P38567603
ARSAGAL3ST1Q99999581

IntAct

91 interactions, top by confidence:

ABTypeScore
ARSATRIP13psi-mi:“MI:0915”(physical association)0.900
TRIP13ARSApsi-mi:“MI:0915”(physical association)0.900
KLK5DENND11psi-mi:“MI:0914”(association)0.640
SCGB1D1MANBApsi-mi:“MI:0914”(association)0.640
C22orf39ARSApsi-mi:“MI:0915”(physical association)0.560
ENKD1ARSApsi-mi:“MI:0915”(physical association)0.560
ARSAC22orf39psi-mi:“MI:0915”(physical association)0.560
ARSAPKN1psi-mi:“MI:0915”(physical association)0.560
ARSAENKD1psi-mi:“MI:0915”(physical association)0.560
CCDC22ARSApsi-mi:“MI:0915”(physical association)0.560
ARSACAMK2Bpsi-mi:“MI:0915”(physical association)0.560
PROP1ARSApsi-mi:“MI:0915”(physical association)0.560
ARSAEID2Bpsi-mi:“MI:0915”(physical association)0.560
ARSAPOU1F1psi-mi:“MI:0915”(physical association)0.560
ARSAANXA11psi-mi:“MI:0915”(physical association)0.560
ARSAFOXI1psi-mi:“MI:0915”(physical association)0.560
VENTXARSApsi-mi:“MI:0915”(physical association)0.560
ARSARHOXF2psi-mi:“MI:0915”(physical association)0.560

BioGRID (99): TRIP13 (Two-hybrid), ARSA (Affinity Capture-MS), ARSA (Affinity Capture-MS), ARSA (Affinity Capture-MS), SUMF1 (Affinity Capture-MS), GALNS (Affinity Capture-MS), MESDC2 (Affinity Capture-MS), ZBTB43 (Affinity Capture-MS), PDIA5 (Affinity Capture-MS), PPOX (Affinity Capture-MS), GFPT2 (Affinity Capture-MS), TRIP13 (Two-hybrid), TRIP13 (Two-hybrid), SUMF1 (Affinity Capture-MS), ZBTB43 (Affinity Capture-MS)

ESM2 similar proteins: A0A0U1RPR8, O18835, O19179, O62763, O77695, O88941, O97524, P08236, P10253, P14000, P15289, P15589, P15848, P21836, P22303, P22412, P23795, P26010, P33727, P37136, P50427, P50428, P50429, P50430, P50473, P51688, P51689, P51690, P51839, P51840, P52785, P54793, Q02846, Q08DD1, Q13724, Q29499, Q32KH8, Q32KH9, Q32KJ9, Q3TYD4

Diamond homologs: P08842, P14000, P15289, P15589, P20713, P34059, P50427, P50428, P50473, P51689, P51690, P54793, Q08DD1, Q32KH5, Q32KH8, Q32KH9, Q32KJ6, Q32KJ9, Q3TYD4, Q571E4, Q5FYA8, Q5FYB0, Q60HH5, Q8BM89, Q8WNQ7, Q9X759, T2KMG4, T2KN90, P22304, P31447, Q08890, Q32KI9, Q32KJ8, Q5FYB1, Q96EG1, P33727, P50430, Q32KH7, Q8A2F6, Q8A2H2

SIGNOR signaling

2 interactions.

AEffectBMechanism
ARSA“up-regulates activity”HBBacetylation
ARSA“up-regulates activity”HBA1acetylation

Disease & clinical

Clinical variants and AI predictions

ClinVar

1329 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic164
Likely pathogenic134
Uncertain significance375
Likely benign429
Benign46

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
1041453NM_000487.6(ARSA):c.385G>A (p.Gly129Arg)Pathogenic
1068641NM_000487.6(ARSA):c.685-2A>GPathogenic
1070652NM_000487.6(ARSA):c.1107+1G>TPathogenic
1072391NC_000022.10:g.(?51063563)(51066217_?)delPathogenic
1072392NC_000022.10:g.(?51064344)(51066227_?)delPathogenic
1098313NM_000487.6(ARSA):c.582del (p.Trp195fs)Pathogenic
1177268NM_000487.6(ARSA):c.1228_1229del (p.Thr410fs)Pathogenic
1210332NM_000487.6(ARSA):c.488G>C (p.Cys163Ser)Pathogenic
1323434NM_000487.6(ARSA):c.208_209del (p.Leu70fs)Pathogenic
1381264NM_000487.6(ARSA):c.731C>A (p.Ser244Ter)Pathogenic
1406153NM_000487.6(ARSA):c.272del (p.Pro91fs)Pathogenic
1421225NM_000487.6(ARSA):c.270C>A (p.Tyr90Ter)Pathogenic
1436884NM_000487.6(ARSA):c.157_164del (p.Gln53fs)Pathogenic
1452278NM_000487.6(ARSA):c.1136del (p.Pro379fs)Pathogenic
1452818NM_000487.6(ARSA):c.617dup (p.Ala207fs)Pathogenic
1455014NC_000022.10:g.(?51065065)(51065595_?)delPathogenic
1455794NM_000487.6(ARSA):c.302_303delinsTT (p.Gly101Val)Pathogenic
1457224NM_000487.6(ARSA):c.1293T>A (p.Tyr431Ter)Pathogenic
1460113NM_000487.6(ARSA):c.13del (p.Ala5fs)Pathogenic
1476243NM_000487.6(ARSA):c.393_425del (p.Pro132_Gly142del)Pathogenic
1685545NM_000487.6(ARSA):c.1228dup (p.Thr410fs)Pathogenic
1707612NM_000487.6(ARSA):c.1030del (p.Ala344fs)Pathogenic
1707618NM_000487.6(ARSA):c.891_895del (p.Gly298fs)Pathogenic
188949NM_000487.6(ARSA):c.979+1G>APathogenic
188976NM_000487.6(ARSA):c.240dup (p.Gly81fs)Pathogenic
189073NM_000487.6(ARSA):c.304del (p.Leu102fs)Pathogenic
189170NM_000487.6(ARSA):c.1223_1231del (p.Ser408_Thr410del)Pathogenic
1956862NM_000487.6(ARSA):c.311del (p.Leu104fs)Pathogenic
1963676NM_000487.6(ARSA):c.245G>T (p.Arg82Leu)Pathogenic
1982373NM_000487.6(ARSA):c.263del (p.Gly88fs)Pathogenic

SpliceAI

1823 predictions. Top by Δscore:

VariantEffectΔscore
22:50625577:AC:Adonor_gain1.0000
22:50625931:CCTA:Cdonor_loss1.0000
22:50625932:CTA:Cdonor_loss1.0000
22:50625933:TACCT:Tdonor_loss1.0000
22:50625934:A:ATdonor_loss1.0000
22:50625935:C:Tdonor_loss1.0000
22:50626061:CGC:Cacceptor_gain1.0000
22:50626828:ACTT:Adonor_loss1.0000
22:50626830:TTA:Tdonor_loss1.0000
22:50626832:A:ACdonor_gain1.0000
22:50626833:C:CAdonor_gain1.0000
22:50626833:CG:Cdonor_gain1.0000
22:50626833:CGT:Cdonor_gain1.0000
22:50626833:CGTG:Cdonor_gain1.0000
22:50626833:CGTGA:Cdonor_gain1.0000
22:50627007:C:CTacceptor_gain1.0000
22:50627021:G:Tacceptor_gain1.0000
22:50627268:T:TAdonor_gain1.0000
22:50627550:CTTTA:Cdonor_loss1.0000
22:50627551:TTTAC:Tdonor_loss1.0000
22:50627552:TTA:Tdonor_loss1.0000
22:50627553:TAC:Tdonor_loss1.0000
22:50627891:C:CAdonor_gain1.0000
22:50627911:T:TAdonor_gain1.0000
22:50625607:T:Adonor_gain0.9900
22:50626060:ACGCC:Aacceptor_loss0.9900
22:50626062:GCCTG:Gacceptor_loss0.9900
22:50626063:CCTG:Cacceptor_loss0.9900
22:50626064:C:CCacceptor_gain0.9900
22:50626064:CTGG:Cacceptor_loss0.9900

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000378031 (22:50626508 T>C), RS1000431855 (22:50626306 A>G,T), RS1000715285 (22:50627582 C>G,T), RS1000766642 (22:50627401 G>A), RS1000945488 (22:50623060 G>C), RS1001100248 (22:50625684 G>A,C), RS1001331166 (22:50623846 C>T), RS1001680534 (22:50624044 C>T), RS1002298028 (22:50625623 A>G), RS1002388779 (22:50628560 C>G), RS1002426091 (22:50629817 C>T), RS1002441093 (22:50628330 G>C,T), RS1002825563 (22:50628738 T>G), RS1002909590 (22:50630048 A>G), RS1003164509 (22:50628535 A>G)

Disease associations

OMIM: gene MIM:607574 | disease phenotypes: MIM:250100, MIM:108600, MIM:312080, MIM:619418, MIM:215700

GenCC curated gene-disease

DiseaseClassificationInheritance
metachromatic leukodystrophy, juvenile formDefinitiveAutosomal recessive
metachromatic leukodystrophyDefinitiveAutosomal recessive

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
metachromatic leukodystrophyDefinitiveAR

Mondo (15): metachromatic leukodystrophy (MONDO:0018868), neurodevelopmental disorder (MONDO:0700092), metachromatic leukodystrophy, juvenile form (MONDO:0009591), metachromatic leukodystrophy, late infantile form (MONDO:0017729), lysosomal storage disease (MONDO:0002561), intellectual disability (MONDO:0001071), metachromatic leukodystrophy, adult form (MONDO:0017730), congenital nervous system disorder (MONDO:0002320), spastic ataxia (MONDO:0017845), leukodystrophy (MONDO:0019046), primary amenorrhea (MONDO:1060208), autosomal recessive sideroblastic anemia (MONDO:0016828), frontotemporal dementia (MONDO:0017276), neurologic, endocrine, and pancreatic disease, multisystem, infantile-onset 2 (MONDO:0030375), citrullinemia (MONDO:0015991)

Orphanet (11): Metachromatic leukodystrophy (Orphanet:512), Metachromatic leukodystrophy, juvenile form (Orphanet:309263), Metachromatic leukodystrophy, late infantile form (Orphanet:309256), Lysosomal disease (Orphanet:68366), Metachromatic leukodystrophy, adult form (Orphanet:309271), Spastic ataxia (Orphanet:316226), Leukodystrophy (Orphanet:68356), Autosomal recessive sideroblastic anemia (Orphanet:260305), Frontotemporal dementia (Orphanet:282), Citrullinemia (Orphanet:187), NON RARE IN EUROPE: Unexplained intellectual disability (Orphanet:319658)

HPO phenotypes

66 total (30 of 66 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000020Urinary incontinence
HP:0000648Optic atrophy
HP:0000649Abnormality of visual evoked potentials
HP:0000712Emotional lability
HP:0000716Depression
HP:0000726Dementia
HP:0000736Short attention span
HP:0000738Hallucinations
HP:0000746Delusion
HP:0000762Decreased nerve conduction velocity
HP:0001082Cholecystitis
HP:0001249Intellectual disability
HP:0001250Seizure
HP:0001251Ataxia
HP:0001252Hypotonia
HP:0001257Spasticity
HP:0001260Dysarthria
HP:0001265Hyporeflexia
HP:0001268Mental deterioration
HP:0001283Bulbar palsy
HP:0001288Gait disturbance
HP:0001290Generalized hypotonia
HP:0001324Muscle weakness
HP:0001332Dystonia
HP:0001347Hyperreflexia
HP:0001939Abnormality of metabolism/homeostasis
HP:0002066Gait ataxia
HP:0002072Chorea
HP:0002080Intention tremor

GWAS associations

6 associations (top):

StudyTraitp-value
GCST002147_20Fibrinogen3.000000e-08
GCST004122_13Fibrinogen levels3.000000e-08
GCST004642_2QT interval (ambient particulate matter interaction)1.000000e-06
GCST007447_2vWF and FVIII levels5.000000e-08
GCST009733_93Urinary metabolite levels in chronic kidney disease9.000000e-13
GCST90011899_89Aspartate aminotransferase levels2.000000e-14

EFO canonical traits (5, from GWAS)

EFO IDTrait name
EFO:0004682QT interval
EFO:0008255particulate matter air pollution measurement
EFO:0004630factor VIII measurement
EFO:0005116urinary metabolite measurement
EFO:0004736aspartate aminotransferase measurement

MeSH disease descriptors (7)

DescriptorNameTree numbers
D020159CitrullinemiaC10.228.140.163.100.937.374; C16.320.565.100.940.374; C16.320.565.189.937.374; C18.452.132.100.937.374; C18.452.648.100.940.374; C18.452.648.189.937.374
D057180Frontotemporal DementiaC10.228.140.380.266.299; C10.574.950.300.299; C18.452.845.800.300.299; F03.615.400.380.299
D008607Intellectual DisabilityC10.597.606.360; C23.888.592.604.646; F01.700.687; F03.625.539
D007966Leukodystrophy, MetachromaticC10.228.140.163.100.362.550; C10.228.140.163.100.435.825.850.500; C10.228.140.695.625.550; C10.314.400.550; C16.320.565.189.362.550; C16.320.565.189.435.825.850.500; C16.320.565.398.641.803.925.500; C16.320.565.595.554.825.850.500; C18.452.132.100.362.550; C18.452.132.100.435.825.850.500; C18.452.584.563.641.803.925.500; C18.452.648.189.362.550; C18.452.648.189.435.825.850.500; C18.452.648.398.641.803.925.500; C18.452.648.595.554.825.850.500
D016464Lysosomal Storage DiseasesC16.320.565.595; C18.452.648.595
D065886Neurodevelopmental DisordersF03.625
C564815Spastic Ataxia (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL2193 (SINGLE PROTEIN)

PharmGKB: 1 entry (VIP=true, CPIC=false)

PharmGKB clinical annotations

1 annotations.

VariantTypeLevelDrugsPhenotypes
rs2071421Efficacy3methylphenidateAttention Deficit Disorder with Hyperactivity

PharmGKB variants

1 variants.

VariantGenesLevelScore#Clin annotsDrugs
rs2071421ARSA30.001methylphenidate

CTD chemical–gene interactions

33 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneincreases methylation, increases mutagenesis2
Tobacco Smoke Pollutionaffects expression, increases expression2
aristolochic acid Idecreases expression1
GSK-J4decreases expression1
triphenyl phosphateaffects expression1
bisphenol Aincreases expression1
glycidyl methacrylatedecreases expression1
sodium arseniteincreases expression1
perfluorooctanoic acidincreases expression1
perfluorooctane sulfonic acidincreases expression1
CD 437decreases expression1
3-(4’-hydroxy-3’-adamantylbiphenyl-4-yl)acrylic aciddecreases expression1
nutlin 3affects cotreatment, increases expression, increases secretion1
bisphenol Bincreases expression1
jinfukangaffects cotreatment, increases expression1
(+)-JQ1 compoundincreases expression1
MT19c compounddecreases expression1
bisphenol AFincreases expression1
Air Pollutantsaffects expression, increases abundance1
Calcitriolincreases expression, affects cotreatment1
Cisplatinaffects cotreatment, increases expression1
Dactinomycinaffects cotreatment, increases expression, increases secretion1
Dichlorodiphenyl Dichloroethylenedecreases expression1
Diazinonincreases methylation1
Diethylhexyl Phthalatedecreases expression1
Ozoneaffects expression, increases abundance1
Quercetinincreases expression1
Smokedecreases expression1
Testosteroneaffects cotreatment, increases expression1
Tetrachlorodibenzodioxinaffects expression1

ChEMBL screening assays

4 unique, capped per target: 3 binding, 1 functional

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL3215185FunctionalPubChem BioAssay. qHTS screen for enhancers of Arylsulfatase A (ASA1): LOPAC Validation Assay. (Class of assay: confirmatory)PubChem BioAssay data set
CHEMBL5098109BindingInhibition of ARSA (unknown origin) using 4-methylumbelliferyl sulfate (4-MUS) as a substrate by fluorescent assayRecent advances of quinones as a privileged structure in drug discovery. — Eur J Med Chem

Cellosaurus cell lines

7 cell lines: 4 cancer cell line, 1 finite cell line, 1 induced pluripotent stem cell, 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_6B33GM00197Finite cell lineMale
CVCL_A4WIMPIi007-AInduced pluripotent stem cellMale
CVCL_D1LJAbcam K-562 ARSA KOCancer cell lineFemale
CVCL_D2I5Abcam Raji ARSA KOCancer cell lineMale
CVCL_D5F7HeLa::TMEM192-3xHA ARSA partial KOCancer cell lineFemale
CVCL_UQ16Abcam Jurkat ARSA KOCancer cell lineMale
CVCL_YP18ARSA-/- immortalized MSCTransformed cell lineSex unspecified

Clinical trials (associated diseases)

263 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT04586348PHASE4UNKNOWNPrenatal Iodine Supplementation and Early Childhood Neurodevelopment
NCT04873115PHASE4UNKNOWNDouble-blind, Placebo-controlled, Randomized Clinical Trial Comparing the Efficacy and Safety of Sialanar Plus orAl rehabiLitation Against Placebo Plus Oral Rehabilitation for chIldren and Adolescents With seVere Sialorrhoea and Neurodisabilties,
NCT04283227PHASE3ACTIVE_NOT_RECRUITINGOTL-200 in Patients With Late Juvenile Metachromatic Leukodystrophy (MLD)
NCT02559102PHASE3COMPLETEDDexmedetomidine Sedation Versus General Anaesthesia for Inguinal Hernia Surgery in Infants
NCT02757079PHASE3COMPLETEDStudy of the Efficacy and Safety of NPC-15 for Sleep Disorders of Children With Neurodevelopmental Disorders
NCT06915480PHASE3RECRUITINGReducing Missed Appointments
NCT07377032PHASE3RECRUITINGTAP-GRIN: Interventional Study on Patients With GRIN-related Neurodevelopmental Disorders
NCT00654433PHASE3TERMINATEDALD-101 Adjuvant Therapy of Unrelated Umbilical Cord Blood Transfusion (UCBT) in Patients With Inherited Metabolic Diseases
NCT00383448PHASE2COMPLETEDHSCT for High Risk Inherited Inborn Errors
NCT01043640PHASE2COMPLETEDAllogeneic Bone Marrow Transplant for Inherited Metabolic Disorders
NCT01303146PHASE2COMPLETEDEfficacy METAZYM for the Treatment Metachromatic Leukodystrophy Treated With Hematopoietic Stem Cell Transplantation
NCT02171104PHASE2ACTIVE_NOT_RECRUITINGMT2013-31: Allo HCT for Metabolic Disorders and Severe Osteopetrosis
NCT03392987PHASE2COMPLETEDA Safety and Efficacy Study of Cryopreserved OTL-200 for Treatment of Metachromatic Leukodystrophy (MLD)
NCT03771898PHASE2ACTIVE_NOT_RECRUITINGA Study of Intrathecal SHP611 in Children With Metachromatic Leukodystrophy
NCT02909959PHASE2COMPLETEDSulforaphane for the Treatment of Young Men With Autism Spectrum Disorder
NCT06081348PHASE2RECRUITINGSertraline vs. Placebo in the Treatment of Anxiety in Children and AdoLescents With NeurodevelopMental Disorders
NCT06352372PHASE2COMPLETEDSafety and Efficacy of tPBM for Epileptiform Activity in Autism
NCT06130228PHASE2UNKNOWNNutritional Therapy in Late-onset Pompe Disease
NCT00418561PHASE1COMPLETEDMetazym for the Treatment of Patients With Late Infantile Metachromatic Leukodystrophy (MLD)
NCT01586455PHASE1COMPLETEDHuman Placental-Derived Stem Cell Transplantation
NCT00503191PHASE1COMPLETEDNeuroModulation Technique Treatment of Autism
NCT04475848PHASE1COMPLETEDA Study to Investigate the Safety, Tolerability, Pharmacokinetics, Pharmacodynamics and Food Effect of RO6953958 in Healthy Participants
NCT06300398PHASE1COMPLETEDIAMA-6 Oral Dose Study in Healthy Adults
NCT00215527PHASE1TERMINATEDIntrathecal Enzyme Replacement Therapy for Spinal Cord Compression in Mucopolysaccharidosis (MPS) I
NCT00744692PHASE1COMPLETEDReduced Intensity Conditioning for Umbilical Cord Blood Transplant in Pediatric Patients With Non-Malignant Disorders
NCT00786968PHASE1TERMINATEDExtension Study of Intrathecal Enzyme Replacement Therapy for MPS I
NCT01003912PHASE1WITHDRAWNFetal Umbilical Cord Blood (UCB) Transplant for Lysosomal Storage Diseases
NCT02699190Not specifiedCOMPLETEDLeukoSEQ: Whole Genome Sequencing as a First-Line Diagnostic Tool for Leukodystrophies
NCT03047369Not specifiedRECRUITINGThe Myelin Disorders Biorepository Project
NCT03333200Not specifiedRECRUITINGLongitudinal Study of Neurodegenerative Disorders
NCT05119764Not specifiedCOMPLETEDManual Lymphatic Drainage Before and After Total Knee Replacement, a Single-center Observer-blinded Randomized Controlled Trial
NCT00176904PHASE2/PHASE3COMPLETEDStem Cell Transplant for Inborn Errors of Metabolism
NCT01372228PHASE1/PHASE2TERMINATEDPhase I/II Pilot Study of Mixed Chimerism to Treat Inherited Metabolic Disorders
NCT01510028PHASE1/PHASE2COMPLETEDMulticenter Study of HGT-1110 Administered Intrathecally in Children With Metachromatic Leukodystrophy (MLD)
NCT01560182PHASE1/PHASE2COMPLETEDGene Therapy for Metachromatic Leukodystrophy (MLD)
NCT01801709PHASE1/PHASE2COMPLETEDIntracerebral Gene Therapy for Children With Early Onset Forms of Metachromatic Leukodystrophy
NCT01887938PHASE1/PHASE2COMPLETEDAn Efficacy and Safety Study of HGT-1110 in Participants With Metachromatic Leukodystrophy
NCT02559830PHASE1/PHASE2UNKNOWNAutologous Hematopoietic Stem Cell Gene Therapy for Metachromatic Leukodystrophy and Adrenoleukodystrophy
NCT00004378Not specifiedCOMPLETEDStem Cell Transplantation (SCT) for Genetic Diseases
NCT00005900Not specifiedUNKNOWNStudy of Pulmonary Complications in Pediatric Patients With Storage Disorders Undergoing Allogeneic Hematopoietic Stem Cell Transplantation