ARSH

arylsulfatase family member H, the group of Sulfatases

Basic information

Region (hg38): X:3006546-3034111

Links

ENSG00000205667 ∙ NCBI:347527 ∙ OMIM:300586 ∙ HGNC:32488 ∙ Uniprot:Q5FYA8 ∙ 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 ARSH gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARSH 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		1
missense			27	1	4	32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	2	4

Variants in ARSH

This is a list of pathogenic ClinVar variants found in the ARSH 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-3006595-G-A		ARSH-related condition	Likely benign (Sep 09, 2024)
X-3006636-C-G		not specified	Uncertain significance (Jan 30, 2024)
X-3006652-G-A		not specified	Uncertain significance (Jun 21, 2021)
X-3006688-G-A		not specified	Uncertain significance (Jun 07, 2024)
X-3010047-G-A			Benign (Jul 26, 2018)
X-3010084-C-T			Benign (-)
X-3010129-C-T			Benign (-)
X-3010130-G-A		not specified	Uncertain significance (Oct 25, 2023)
X-3010133-C-T		not specified	Conflicting classifications of pathogenicity (Mar 01, 2023)
X-3010142-A-G		not specified	Uncertain significance (Jul 19, 2023)
X-3013071-A-G		not specified	Uncertain significance (Dec 02, 2021)
X-3013151-G-A		not specified	Uncertain significance (Dec 02, 2022)
X-3013157-C-T		not specified	Uncertain significance (Nov 10, 2022)
X-3013161-C-A		not specified	Uncertain significance (Jul 14, 2021)
X-3013190-T-G			Likely benign (-)
X-3015002-C-T		not specified	Uncertain significance (Dec 28, 2022)
X-3015014-T-C		not specified	Uncertain significance (Aug 04, 2021)
X-3015016-T-C			Benign (-)
X-3015025-G-C			Likely benign (-)
X-3015057-T-G			Likely benign (May 17, 2017)
X-3015059-C-A			Benign (May 14, 2018)
X-3015110-C-T		not specified	Uncertain significance (Feb 28, 2024)
X-3015191-C-T		not specified	Uncertain significance (Apr 18, 2024)
X-3015192-G-A			Likely benign (-)
X-3015270-G-A			Benign (-)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARSH	protein_coding	protein_coding	ENST00000381130	9	26959

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.32e-8	0.281	125676	21	48	125745	0.000274

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.314	216	229	0.942	0.0000185	3653
Missense in Polyphen		82	79.145	1.0361		1312
Synonymous	0.876	82	92.7	0.884	0.00000800	1114
Loss of Function	0.478	12	13.9	0.862	9.37e-7	239

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00102	0.000861
Ashkenazi Jewish	0.00	0.00
East Asian	0.000217	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000334	0.000229
Middle Eastern	0.000217	0.000163
South Asian	0.00131	0.000752
Other	0.000221	0.000163

dbNSFP

Source: dbNSFP

• 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)

Intolerance Scores

• loftool: 0.223
• rvis_EVS: 1.45
• rvis_percentile_EVS: 95.12

Haploinsufficiency Scores

• pHI: 0.0630
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0926

Gene Damage Prediction

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

Gene ontology

• Cellular component: endoplasmic reticulum lumen;integral component of membrane
• Molecular function: arylsulfatase activity;metal ion binding