HS3ST1

heparan sulfate-glucosamine 3-sulfotransferase 1, the group of Sulfotransferases, membrane bound

Basic information

Region (hg38): 4:11393150-11429564

Links

ENSG00000002587 ∙ NCBI:9957 ∙ OMIM:603244 ∙ HGNC:5194 ∙ Uniprot:O14792 ∙ 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 HS3ST1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HS3ST1 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						0
missense			18	1		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	1	0

Variants in HS3ST1

This is a list of pathogenic ClinVar variants found in the HS3ST1 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-11399161-A-G		not specified	Uncertain significance (Jun 28, 2022)
4-11399162-G-A		not specified	Uncertain significance (Dec 13, 2022)
4-11399171-G-A		not specified	Uncertain significance (Aug 04, 2023)
4-11399172-A-T		not specified	Uncertain significance (May 14, 2024)
4-11399215-C-A		not specified	Uncertain significance (Jun 28, 2023)
4-11399234-G-A		not specified	Uncertain significance (Aug 13, 2021)
4-11399243-A-G		not specified	Uncertain significance (Dec 15, 2023)
4-11399327-C-T		not specified	Uncertain significance (Mar 16, 2022)
4-11399417-G-C		not specified	Uncertain significance (Dec 21, 2022)
4-11399452-T-A		not specified	Uncertain significance (Feb 05, 2024)
4-11399558-A-T		not specified	Uncertain significance (Jan 31, 2022)
4-11399584-C-T		not specified	Uncertain significance (Sep 20, 2023)
4-11399615-C-T		not specified	Uncertain significance (Apr 07, 2022)
4-11399647-G-T		not specified	Uncertain significance (Jul 14, 2023)
4-11399684-G-A		not specified	Uncertain significance (Apr 26, 2023)
4-11399717-T-C		not specified	Likely benign (Dec 14, 2021)
4-11399756-C-T		not specified	Uncertain significance (May 18, 2022)
4-11399939-C-T		not specified	Uncertain significance (Aug 12, 2021)
4-11399969-C-T		not specified	Uncertain significance (Dec 14, 2021)
4-11399987-C-G		not specified	Uncertain significance (Nov 30, 2021)
4-11406961-T-C		Arteriosclerosis disorder;Coronary artery disorder	risk factor (May 11, 2014)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HS3ST1	protein_coding	protein_coding	ENST00000002596	1	36616

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00443	0.882	125735	0	13	125748	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.09	171	216	0.792	0.0000156	2008
Missense in Polyphen		52	96.177	0.54067		868
Synonymous	0.599	96	104	0.925	0.00000823	621
Loss of Function	1.34	5	9.44	0.529	5.74e-7	90

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000145	0.000145
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000528	0.0000527
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
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 position 3 of glucosamine residues in heparan. Catalyzes the rate limiting step in the biosynthesis of heparan sulfate (HSact). This modification is a crucial step in the biosynthesis of anticoagulant heparan sulfate as it completes the structure of the antithrombin pentasaccharide binding site. {ECO:0000269|PubMed:9346953}.
• 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: 0.132

Intolerance Scores

• rvis_EVS: -0.43
• rvis_percentile_EVS: 25.37

Haploinsufficiency Scores

• pHI: 0.0725
• hipred: Y
• hipred_score: 0.546
• ghis: 0.586

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.341

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hs3st1
• Phenotype: embryo 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); growth/size/body region phenotype

Gene ontology

• Biological process: glycosaminoglycan biosynthetic process;heparan sulfate proteoglycan biosynthetic process
• Cellular component: Golgi lumen
• Molecular function: sulfotransferase activity;[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity;heparan sulfate sulfotransferase activity