SULF1

sulfatase 1, the group of Sulfatases

Basic information

Region (hg38): 8:69466624-69660915

Links

ENSG00000137573 ∙ NCBI:23213 ∙ OMIM:610012 ∙ HGNC:20391 ∙ Uniprot:Q8IWU6 ∙ 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 SULF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SULF1 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	60	5	67
missense			145	5	4	154
nonsense			4			4
start loss						0
frameshift			1			1
inframe indel			2		1	3
splice donor/acceptor (+/-2bp)			1			1
splice region			7	7	1	15
non coding			1	31	17	49
Total	0	0	156	96	27

Variants in SULF1

This is a list of pathogenic ClinVar variants found in the SULF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-69563980-A-G			Uncertain significance (Jun 22, 2022)
8-69563986-C-T		not specified	Uncertain significance (Mar 01, 2023)
8-69563996-T-C			Likely benign (Oct 28, 2023)
8-69564031-G-A			Uncertain significance (Sep 17, 2022)
8-69564037-T-A		not specified	Uncertain significance (Dec 19, 2022)
8-69564043-C-A			Uncertain significance (Oct 28, 2022)
8-69564043-C-T		not specified	Uncertain significance (May 23, 2023)
8-69564044-G-A			Likely benign (Nov 21, 2023)
8-69564051-A-G			Uncertain significance (Aug 20, 2022)
8-69564055-C-T			Uncertain significance (May 22, 2023)
8-69564088-G-A			Uncertain significance (May 03, 2022)
8-69564089-A-C			Likely benign (May 29, 2021)
8-69564095-C-T			Likely benign (Aug 30, 2023)
8-69564100-G-A			Uncertain significance (Nov 25, 2023)
8-69564126-G-A		not specified	Uncertain significance (May 08, 2023)
8-69575959-G-A			Likely benign (May 30, 2023)
8-69575978-C-A		not specified	Uncertain significance (Jan 18, 2024)
8-69575986-G-C			Uncertain significance (Dec 03, 2021)
8-69575994-C-T			Uncertain significance (Jul 06, 2022)
8-69575995-G-A			Likely benign (Jul 09, 2022)
8-69576013-TG-T			Uncertain significance (Dec 26, 2022)
8-69576016-G-A			Likely benign (Jul 03, 2023)
8-69576016-G-C			Likely benign (Jul 17, 2023)
8-69576016-G-T			Likely benign (Oct 21, 2022)
8-69576020-G-A			Uncertain significance (Feb 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SULF1	protein_coding	protein_coding	ENST00000260128	19	194292

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00138	0.999	125715	0	33	125748	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.51	414	510	0.812	0.0000293	5794
Missense in Polyphen		109	169.93	0.64143		1864
Synonymous	-0.430	195	188	1.04	0.0000112	1562
Loss of Function	4.59	15	50.1	0.300	0.00000280	575

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000233	0.000233
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000219	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000134	0.000132
Middle Eastern	0.000219	0.000217
South Asian	0.000271	0.000261
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Exhibits arylsulfatase activity and highly specific endoglucosamine-6-sulfatase activity. It can remove sulfate from the C-6 position of glucosamine within specific subregions of intact heparin. Diminishes HSPG (heparan sulfate proteoglycans) sulfation, inhibits signaling by heparin-dependent growth factors, diminishes proliferation, and facilitates apoptosis in response to exogenous stimulation.

Recessive Scores

• pRec: 0.150

Intolerance Scores

• loftool: 0.0170
• rvis_EVS: -0.48
• rvis_percentile_EVS: 22.75

Haploinsufficiency Scores

• pHI: 0.677
• hipred: Y
• hipred_score: 0.554
• ghis: 0.568

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0324

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sulf1
• Phenotype: growth/size/body region phenotype; cellular phenotype; muscle phenotype; vision/eye phenotype; craniofacial phenotype; normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; respiratory system phenotype; immune system phenotype; renal/urinary system phenotype; skeleton phenotype; limbs/digits/tail 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); digestive/alimentary phenotype

Zebrafish Information Network

• Gene name: sulf1
• Affected structure: muscle cell
• Phenotype tag: abnormal
• Phenotype quality: sparse

Gene ontology

• Biological process: kidney development;negative regulation of endothelial cell proliferation;chondrocyte development;glomerular filtration;apoptotic process;positive regulation of vascular endothelial growth factor production;esophagus smooth muscle contraction;negative regulation of angiogenesis;positive regulation of Wnt signaling pathway;heparan sulfate proteoglycan metabolic process;negative regulation of cell migration;positive regulation of BMP signaling pathway;glomerular basement membrane development;glial cell-derived neurotrophic factor receptor signaling pathway;regulation of fibroblast growth factor receptor signaling pathway;negative regulation of fibroblast growth factor receptor signaling pathway;vascular endothelial growth factor receptor signaling pathway;embryonic skeletal system development;cartilage development;bone development;innervation;negative regulation of prostatic bud formation
• Cellular component: extracellular space;endoplasmic reticulum;Golgi apparatus;Golgi stack;plasma membrane;cell surface;membrane raft;collagen-containing extracellular matrix
• Molecular function: arylsulfatase activity;calcium ion binding;glycosaminoglycan binding;N-acetylglucosamine-6-sulfatase activity