SULF2

sulfatase 2, the group of Sulfatases

Basic information

Region (hg38): 20:47656196-47786616

Links

ENSG00000196562 ∙ NCBI:55959 ∙ OMIM:610013 ∙ HGNC:20392 ∙ Uniprot:Q8IWU5 ∙ 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 SULF2 gene.

• Inborn genetic diseases (51 variants)
• not provided (8 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SULF2 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				3	2	5
missense			49	3	1	53
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	49	6	3

Variants in SULF2

This is a list of pathogenic ClinVar variants found in the SULF2 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-47661793-C-T		not specified	Uncertain significance (Dec 13, 2021)
20-47661845-C-T		not specified	Uncertain significance (Aug 12, 2021)
20-47661855-G-T		not specified	Uncertain significance (Dec 15, 2022)
20-47663080-T-C		not specified	Uncertain significance (Jul 29, 2022)
20-47663093-C-T		not specified	Uncertain significance (Jul 20, 2021)
20-47663149-T-C		not specified	Uncertain significance (Jun 26, 2023)
20-47663162-T-G		not specified	Uncertain significance (Jan 03, 2024)
20-47663191-G-T		not specified	Uncertain significance (Dec 19, 2022)
20-47663456-T-A		not specified	Uncertain significance (May 03, 2023)
20-47663466-C-T			Likely benign (Jul 06, 2018)
20-47663467-G-A		not specified	Uncertain significance (Jul 26, 2022)
20-47663474-G-T		not specified	Uncertain significance (Feb 23, 2023)
20-47663617-C-T			Likely benign (Jul 10, 2018)
20-47664166-C-T			Benign (Jul 23, 2018)
20-47664171-T-A		not specified	Uncertain significance (Jun 24, 2022)
20-47664182-T-C		not specified	Likely benign (May 05, 2023)
20-47664187-T-C		not specified	Uncertain significance (Dec 01, 2022)
20-47665200-T-C		not specified	Uncertain significance (Mar 11, 2022)
20-47665250-C-T		not specified	Uncertain significance (Mar 14, 2023)
20-47665859-C-T		not specified	Uncertain significance (Oct 05, 2021)
20-47665939-T-A		not specified	Uncertain significance (Jul 09, 2021)
20-47666256-T-C			Benign (Jul 30, 2018)
20-47666285-C-T		not specified	Uncertain significance (Apr 13, 2022)
20-47666286-G-A			Likely benign (Jun 12, 2018)
20-47666297-C-T		not specified	Uncertain significance (Jul 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SULF2	protein_coding	protein_coding	ENST00000359930	20	130269

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0106	0.989	125724	0	24	125748	0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.72	442	556	0.795	0.0000368	5733
Missense in Polyphen		169	255.19	0.66225		2624
Synonymous	0.255	225	230	0.979	0.0000166	1593
Loss of Function	4.57	13	46.7	0.278	0.00000240	533

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000216	0.000210
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000333	0.000326
Finnish	0.0000465	0.0000462
European (Non-Finnish)	0.0000443	0.0000439
Middle Eastern	0.000333	0.000326
South Asian	0.000205	0.000196
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.

Intolerance Scores

• loftool: 0.0167
• rvis_EVS: -1.59
• rvis_percentile_EVS: 3.08

Haploinsufficiency Scores

• pHI: 0.147
• hipred: Y
• hipred_score: 0.639
• ghis: 0.510

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.665

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sulf2
• Phenotype: muscle phenotype; craniofacial phenotype; cellular phenotype; growth/size/body region 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); limbs/digits/tail phenotype; digestive/alimentary phenotype; vision/eye phenotype; renal/urinary system phenotype; skeleton phenotype; embryo phenotype; respiratory system phenotype; reproductive system 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)

Gene ontology

• Biological process: kidney development;chondrocyte development;glomerular filtration;response to wounding;positive regulation of vascular endothelial growth factor production;esophagus smooth muscle contraction;positive regulation of Wnt signaling pathway;heparan sulfate proteoglycan metabolic process;glomerular basement membrane development;glial cell-derived neurotrophic factor receptor signaling pathway;negative regulation of fibroblast growth factor receptor signaling pathway;embryonic skeletal system development;cartilage development;bone development;innervation;positive regulation of canonical Wnt signaling pathway;liver regeneration;regulation of hepatocyte proliferation
• Cellular component: extracellular space;endoplasmic reticulum;Golgi stack;plasma membrane;cell surface
• Molecular function: arylsulfatase activity;calcium ion binding;glycosaminoglycan binding;N-acetylglucosamine-6-sulfatase activity