ARSI

arylsulfatase family member I, the group of Sulfatases

Basic information

Region (hg38): 5:150296342-150339307

Links

ENSG00000183876 ∙ NCBI:340075 ∙ OMIM:610009 ∙ HGNC:32521 ∙ Uniprot:Q5FYB1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autosomal recessive spastic paraplegia type 66 (Supportive), mode of inheritance: AR

ClinVar

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

• Spastic paraplegia (104 variants)
• Inborn genetic diseases (26 variants)
• not provided (10 variants)
• Hereditary spastic paraplegia (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARSI 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				25	12	37
missense			73	1	2	76
nonsense			7			7
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	81	27	14

Variants in ARSI

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

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

Position	Type	Phenotype	Significance	ClinVar
5-150297252-G-A		Spastic paraplegia	Uncertain significance (Feb 19, 2020)
5-150297264-G-A		Spastic paraplegia	Uncertain significance (Sep 15, 2022)
5-150297280-G-A		Spastic paraplegia	Likely benign (Jul 12, 2022)
5-150297282-A-AT			Uncertain significance (Jan 31, 2014)
5-150297293-C-T		Spastic paraplegia • not specified	Uncertain significance (Jul 12, 2023)
5-150297296-C-T		Spastic paraplegia • not specified	Uncertain significance (Jul 05, 2023)
5-150297297-G-A		not specified	Uncertain significance (Mar 06, 2023)
5-150297303-G-A		Spastic paraplegia	Uncertain significance (Feb 27, 2022)
5-150297314-C-T		Spastic paraplegia	Uncertain significance (Sep 22, 2019)
5-150297330-C-T		Spastic paraplegia	Uncertain significance (May 08, 2023)
5-150297346-A-G		Spastic paraplegia	Likely benign (Jul 22, 2023)
5-150297349-A-G		Spastic paraplegia	Likely benign (Nov 15, 2022)
5-150297350-C-T		Spastic paraplegia	Uncertain significance (Jun 20, 2022)
5-150297353-G-A		Spastic paraplegia	Uncertain significance (Jan 30, 2024)
5-150297380-A-C		Spastic paraplegia	Uncertain significance (Jan 18, 2024)
5-150297383-T-C		Spastic paraplegia	Uncertain significance (Apr 25, 2018)
5-150297396-G-A		Spastic paraplegia	Uncertain significance (Feb 01, 2022)
5-150297422-G-A		Spastic paraplegia	Uncertain significance (Nov 08, 2017)
5-150297434-C-T		Spastic paraplegia	Uncertain significance (Dec 11, 2019)
5-150297435-G-C		Spastic paraplegia	Uncertain significance (Aug 21, 2018)
5-150297444-C-A		Spastic paraplegia	Uncertain significance (Nov 04, 2017)
5-150297468-G-A		Hereditary spastic paraplegia	Uncertain significance (Mar 07, 2017)
5-150297483-G-A		Spastic paraplegia	Uncertain significance (Jun 29, 2021)
5-150297503-C-G		Spastic paraplegia	Uncertain significance (Jul 06, 2022)
5-150297503-C-T		Spastic paraplegia • not specified	Uncertain significance (Sep 09, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARSI	protein_coding	protein_coding	ENST00000328668	2	42965

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.96e-15	0.0150	125662	0	86	125748	0.000342

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.853	339	386	0.878	0.0000262	3667
Missense in Polyphen		136	166.02	0.81915		1655
Synonymous	0.210	154	157	0.979	0.0000102	1202
Loss of Function	0.0423	22	22.2	0.990	0.00000129	196

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000463	0.000460
Ashkenazi Jewish	0.00	0.00
East Asian	0.000599	0.000598
Finnish	0.000233	0.000231
European (Non-Finnish)	0.000288	0.000281
Middle Eastern	0.000599	0.000598
South Asian	0.000988	0.000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Displays arylsulfatase activity at neutral pH, when co- expressed with SUMF1; arylsulfatase activity is measured in the secretion medium of retinal cell line, but no activity is recorded when measured in cell extracts. {ECO:0000269|PubMed:16500042, ECO:0000269|PubMed:19262745}.
• Pathway: 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: 0.158

Intolerance Scores

• loftool: 0.136
• rvis_EVS: -1.04
• rvis_percentile_EVS: 7.8

Haploinsufficiency Scores

• pHI: 0.122
• hipred: N
• hipred_score: 0.408
• ghis: 0.551

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.352

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arsi

Gene ontology

• Cellular component: extracellular region;endoplasmic reticulum lumen
• Molecular function: arylsulfatase activity;protein binding;metal ion binding