ARSD

arylsulfatase D, the group of Sulfatases

Basic information

Region (hg38): X:2903972-2929349

Links

ENSG00000006756 ∙ NCBI:414 ∙ OMIM:300002 ∙ HGNC:717 ∙ Uniprot:P51689 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARSD 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				2	1	3
missense			29	12	3	44
nonsense				1		1
start loss						0
frameshift			1			1
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				4		4
Total	0	0	30	20	4

Variants in ARSD

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

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

Position	Type	Phenotype	Significance	ClinVar
X-2907318-G-A		not specified	Uncertain significance (May 22, 2023)
X-2907322-G-A			Benign (Mar 29, 2018)
X-2907437-G-T		ARSD-related disorder • not specified	Uncertain significance (Mar 14, 2023)
X-2907438-C-T		ARSD-related disorder • not specified	Uncertain significance (Mar 14, 2023)
X-2907455-G-C		not specified	Uncertain significance (Jun 22, 2023)
X-2907471-G-A		not specified	Uncertain significance (May 08, 2023)
X-2907540-C-T		not specified	Uncertain significance (Jan 12, 2024)
X-2907555-C-T			Benign (Mar 29, 2018)
X-2907585-C-T		not specified	Uncertain significance (Aug 13, 2021)
X-2907624-C-T		not specified	Uncertain significance (Jun 07, 2023)
X-2908724-C-G		not specified	Uncertain significance (Jan 24, 2024)
X-2908745-C-T		not specified	Uncertain significance (Oct 20, 2023)
X-2909889-C-T			Benign (Mar 29, 2018)
X-2909935-C-T		not specified	Uncertain significance (Feb 28, 2024)
X-2910704-T-C		not specified	Uncertain significance (Apr 08, 2024)
X-2910769-T-G		not specified	Uncertain significance (Jun 22, 2024)
X-2914627-A-G		ARSD-related disorder	Likely benign (Jul 31, 2020)
X-2914655-T-C		ARSD-related disorder	Likely benign (Jul 31, 2020)
X-2914674-T-C		ARSD-related disorder	Likely benign (Jul 31, 2020)
X-2914746-A-G		ARSD-related disorder	Likely benign (Jul 31, 2020)
X-2915564-C-T		ARSD-related disorder	Likely benign (Jul 31, 2020)
X-2915565-A-C		not specified	Uncertain significance (May 04, 2023)
X-2915587-A-C			Likely benign (Mar 28, 2018)
X-2915590-A-G			Likely benign (Mar 28, 2018)
X-2915597-C-T		ARSD-related disorder	Likely benign (Jul 31, 2020)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARSD	protein_coding	protein_coding	ENST00000381154	10	25382

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00163	0.973	125687	13	48	125748	0.000243

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.09	199	247	0.805	0.0000211	3811
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00198	0.00198
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000513	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.000223	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Estrogen metabolism;Metabolism of lipids;Post-translational protein modification;Metabolism of proteins;The activation of arylsulfatases;Gamma carboxylation, hypusine formation and arylsulfatase activation;Androgen and estrogen biosynthesis and metabolism;Metabolism;Glycosphingolipid metabolism;Sphingolipid metabolism (Consensus)

Recessive Scores

• pRec: 0.144

Intolerance Scores

• loftool: 0.0885
• rvis_EVS: 0.18
• rvis_percentile_EVS: 66.07

Haploinsufficiency Scores

• pHI: 0.424
• hipred: N
• hipred_score: 0.314
• ghis: 0.478

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Gene ontology

• Cellular component: lysosome;endoplasmic reticulum lumen
• Molecular function: arylsulfatase activity;metal ion binding