HS3ST3B1

heparan sulfate-glucosamine 3-sulfotransferase 3B1, the group of Sulfotransferases, membrane bound

Basic information

Region (hg38): 17:14301081-14349404

Links

ENSG00000125430 ∙ NCBI:9953 ∙ OMIM:604058 ∙ HGNC:5198 ∙ Uniprot:Q9Y662 ∙ 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 HS3ST3B1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HS3ST3B1 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	2
missense			24		1	25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	0	3

Variants in HS3ST3B1

This is a list of pathogenic ClinVar variants found in the HS3ST3B1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-14301523-G-T		not specified	Uncertain significance (Oct 25, 2023)
17-14301535-G-C		not specified	Uncertain significance (Dec 19, 2023)
17-14301540-G-C		not specified	Uncertain significance (May 28, 2024)
17-14301551-C-T			Benign (May 21, 2018)
17-14301552-C-T		not specified	Uncertain significance (May 30, 2024)
17-14301559-T-C		not specified	Uncertain significance (Mar 25, 2024)
17-14301571-T-A			Benign (Jul 16, 2018)
17-14301618-G-C		not specified	Uncertain significance (Dec 21, 2022)
17-14301633-A-G		not specified	Uncertain significance (Dec 09, 2023)
17-14301687-G-T		not specified	Uncertain significance (Jun 18, 2021)
17-14301718-G-T		not specified	Uncertain significance (Mar 16, 2024)
17-14301753-A-T		not specified	Uncertain significance (Sep 06, 2022)
17-14301778-G-C		not specified	Uncertain significance (Dec 19, 2023)
17-14301790-G-T		not specified	Uncertain significance (Aug 17, 2022)
17-14301820-G-A		not specified	Uncertain significance (Mar 19, 2024)
17-14301829-T-C		not specified	Uncertain significance (Jul 25, 2023)
17-14301846-A-T		not specified	Uncertain significance (Aug 12, 2021)
17-14301850-C-G		not specified	Uncertain significance (Jan 06, 2023)
17-14301851-G-A			Benign (Dec 31, 2019)
17-14301916-G-A		not specified	Uncertain significance (Jun 09, 2022)
17-14301939-A-G		not specified	Uncertain significance (Oct 03, 2022)
17-14301985-T-G		not specified	Uncertain significance (Dec 17, 2023)
17-14302037-C-G		not specified	Uncertain significance (Feb 27, 2023)
17-14345080-A-G		not specified	Uncertain significance (Jul 19, 2023)
17-14345096-G-C		not specified	Uncertain significance (Nov 22, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HS3ST3B1	protein_coding	protein_coding	ENST00000360954	2	48322

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.293	0.688	123495	0	5	123500	0.0000202

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.458	223	243	0.917	0.0000146	2490
Missense in Polyphen		68	91.246	0.74524		982
Synonymous	0.626	109	118	0.927	0.00000755	829
Loss of Function	1.98	2	8.09	0.247	3.45e-7	99

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000502	0.0000449
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Sulfotransferase that utilizes 3'-phospho-5'-adenylyl sulfate (PAPS) to catalyze the transfer of a sulfo group to an N- unsubstituted glucosamine linked to a 2-O-sulfo iduronic acid unit on heparan sulfate. Catalyzes the O-sulfation of glucosamine in IdoUA2S-GlcNS and also in IdoUA2S-GlcNH2. The substrate-specific O-sulfation generates an enzyme-modified heparan sulfate which acts as a binding receptor to Herpes simplex virus-1 (HSV-1) and permits its entry. Unlike 3-OST-1, does not convert non- anticoagulant heparan sulfate to anticoagulant heparan sulfate. {ECO:0000269|PubMed:10520990}.
• Pathway: Glycosaminoglycan biosynthesis - heparan sulfate / heparin - Homo sapiens (human);Metapathway biotransformation Phase I and II;Metabolism of carbohydrates;HS-GAG biosynthesis;Heparan sulfate/heparin (HS-GAG) metabolism;Glycosaminoglycan metabolism;heparan sulfate biosynthesis (late stages);heparan sulfate biosynthesis;Metabolism (Consensus)

Recessive Scores

• pRec: 0.111

Haploinsufficiency Scores

• pHI: 0.182
• hipred: N
• hipred_score: 0.321
• ghis: 0.423

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.274

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hs3st3b1

Gene ontology

• Biological process: glycosaminoglycan biosynthetic process;protein sulfation;heparan sulfate proteoglycan biosynthetic process;heparan sulfate proteoglycan biosynthetic process, enzymatic modification
• Cellular component: Golgi membrane;integral component of plasma membrane
• Molecular function: [heparan sulfate]-glucosamine 3-sulfotransferase 1 activity;[heparan sulfate]-glucosamine 3-sulfotransferase 3 activity;heparan sulfate sulfotransferase activity