ARSG

arylsulfatase G, the group of Sulfatases

Basic information

Region (hg38): 17:68259181-68422731

Links

ENSG00000141337 ∙ NCBI:22901 ∙ OMIM:610008 ∙ HGNC:24102 ∙ Uniprot:Q96EG1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Usher syndrome, type 4 (Moderate), mode of inheritance: AR
• Usher syndrome, type 4 (Limited), mode of inheritance: AR
• Usher syndrome type 3 (Supportive), mode of inheritance: AR
• Usher syndrome, type 4 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Usher syndrome, type IV	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Audiologic/Otolaryngologic; Ophthalmologic	29300381; 32455177; 33300174; 33629623
The onset of hearing loss has been described as postlingual

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ARSG gene.

• not provided (351 variants)
• Inborn genetic diseases (26 variants)
• Usher syndrome, type 4 (10 variants)
• ARSG-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARSG 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			1	77	10	88
missense	1		152	6	8	167
nonsense	1		4			5
start loss						0
frameshift	2	2	8			12
inframe indel			3			3
splice donor/acceptor (+/-2bp)	1	1	10			12
splice region	1		7	10	1	19
non coding			16	28	19	63
Total	5	3	194	111	37

Highest pathogenic variant AF is 0.0000723

Variants in ARSG

This is a list of pathogenic ClinVar variants found in the ARSG region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
17-68269116-C-T		not specified	Likely benign (Oct 05, 2022)
17-68269191-G-A		not specified	Uncertain significance (Jan 17, 2024)
17-68270850-G-A		not specified	Uncertain significance (Jul 13, 2021)
17-68271064-C-T		not specified	Uncertain significance (Jan 24, 2024)
17-68271216-A-C		not specified	Uncertain significance (Aug 21, 2023)
17-68271229-G-A		not specified	Uncertain significance (Sep 01, 2021)
17-68271256-G-T		not specified	Uncertain significance (Aug 17, 2022)
17-68271344-G-C			Benign (Dec 31, 2019)
17-68271426-G-A		not specified	Uncertain significance (Dec 06, 2021)
17-68271465-C-T		not specified	Uncertain significance (Jun 24, 2022)
17-68271484-G-C		not specified	Uncertain significance (Nov 15, 2021)
17-68271495-G-A		not specified	Likely benign (Feb 28, 2024)
17-68271504-C-T		not specified	Uncertain significance (Sep 20, 2023)
17-68271513-T-C		not specified	Uncertain significance (Mar 01, 2023)
17-68271579-A-C		not specified	Uncertain significance (Oct 12, 2022)
17-68271583-T-C		not specified	Uncertain significance (Sep 27, 2021)
17-68271593-T-C			Benign (Apr 04, 2018)
17-68271611-G-A			Likely benign (Dec 01, 2022)
17-68272660-C-T		not specified	Uncertain significance (Sep 26, 2022)
17-68272683-A-G		not specified	Uncertain significance (Mar 01, 2023)
17-68272761-C-T		not specified	Uncertain significance (Mar 01, 2024)
17-68273945-C-T		not specified	Likely benign (Jan 23, 2024)
17-68273953-A-G		not specified	Uncertain significance (Dec 17, 2023)
17-68273969-G-T		not specified	Uncertain significance (Oct 10, 2023)
17-68274038-C-T		not specified	Uncertain significance (Dec 15, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARSG	protein_coding	protein_coding	ENST00000448504	11	163550

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.37e-10	0.418	125658	0	90	125748	0.000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.893	274	319	0.859	0.0000185	3399
Missense in Polyphen		96	121.71	0.78873		1236
Synonymous	0.786	115	126	0.911	0.00000809	1069
Loss of Function	1.03	17	22.2	0.765	9.43e-7	258

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000666	0.000666
Ashkenazi Jewish	0.00	0.00
East Asian	0.000707	0.000707
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.000397	0.000396
Middle Eastern	0.000707	0.000707
South Asian	0.000457	0.000457
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Displays arylsulfatase activity at acidic pH with pseudosubstrates, such as p-nitrocatechol sulfate and also, but with lower activity, p-nitrophenyl sulfate and 4- methylumbelliferyl sulfate. {ECO:0000269|PubMed:18283100}.
• Pathway: Lysosome - Homo sapiens (human);Metabolism of lipids;Post-translational protein modification;Metabolism of proteins;The activation of arylsulfatases;Gamma carboxylation, hypusine formation and arylsulfatase activation;Metabolism;Glycosphingolipid metabolism;Sphingolipid metabolism (Consensus)

Recessive Scores

• pRec: 0.126

Intolerance Scores

• loftool: 0.171
• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.75

Haploinsufficiency Scores

• pHI: 0.146
• hipred: N
• hipred_score: 0.248
• ghis: 0.440

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.443

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	High
Cancer	Medium	Medium	High

Mouse Genome Informatics

• Gene name: Arsg
• Phenotype: homeostasis/metabolism phenotype; immune system phenotype; cellular phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system 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); renal/urinary system phenotype

Gene ontology

• Biological process: sulfur compound metabolic process
• Cellular component: extracellular space;lysosome;endoplasmic reticulum;endoplasmic reticulum lumen
• Molecular function: arylsulfatase activity;metal ion binding