HS3ST6

heparan sulfate-glucosamine 3-sulfotransferase 6, the group of Sulfotransferases, membrane bound

Basic information

Region (hg38): 16:1911475-1918415

Previous symbols: [ "HS3ST5" ]

Links

ENSG00000162040 ∙ NCBI:64711 ∙ OMIM:619210 ∙ HGNC:14178 ∙ Uniprot:Q96QI5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Angioedema, hereditary, 8	AD	Allergy/Immunology/Infectious	The condition can involve episodes of angioedema brought on by certain identifiable triggers, and awareness may allow avoidance of triggers, as well as potential medical management	Allergy/Immunology/Infectious	33508266

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the HS3ST6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HS3ST6 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			52			52
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	52	2	0

Variants in HS3ST6

This is a list of pathogenic ClinVar variants found in the HS3ST6 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-1911633-C-A		not specified	Uncertain significance (May 09, 2024)
16-1911673-G-C		Angioedema, hereditary, 8	Uncertain significance (Nov 24, 2023)
16-1911676-C-A		not specified	Uncertain significance (Jan 23, 2024)
16-1911687-C-T		not specified	Uncertain significance (Jun 22, 2021)
16-1911711-T-C		not specified	Uncertain significance (Mar 16, 2024)
16-1911723-C-T		not specified	Uncertain significance (Jan 23, 2023)
16-1911750-T-C		not specified	Uncertain significance (May 05, 2022)
16-1911757-A-G		not specified	Uncertain significance (Dec 16, 2023)
16-1911775-C-T		not specified	Uncertain significance (Aug 08, 2023)
16-1911802-C-T		not specified	Uncertain significance (Nov 07, 2024)
16-1911834-C-T		not specified	Uncertain significance (Nov 25, 2024)
16-1911851-C-T			Likely benign (Mar 01, 2023)
16-1911856-C-T		not specified	Uncertain significance (Nov 07, 2024)
16-1911862-C-T		not specified	Uncertain significance (Feb 07, 2023)
16-1911867-C-G		not specified	Uncertain significance (Mar 01, 2024)
16-1911867-C-T		not specified	Uncertain significance (Apr 25, 2022)
16-1911868-G-A		not specified	Uncertain significance (Jun 23, 2023)
16-1911869-C-A		not specified	Uncertain significance (Dec 16, 2023)
16-1911921-T-G		not specified	Uncertain significance (Dec 13, 2022)
16-1911934-C-A		not specified	Uncertain significance (Jul 27, 2024)
16-1911949-G-A		not specified	Uncertain significance (Oct 01, 2024)
16-1911952-C-T		not specified	Uncertain significance (Oct 26, 2022)
16-1912002-G-T		not specified	Uncertain significance (Sep 14, 2022)
16-1912003-C-A		not specified	Uncertain significance (Dec 28, 2022)
16-1912003-C-T		not specified	Uncertain significance (Dec 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HS3ST6	protein_coding	protein_coding	ENST00000443547	2	6978

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.436	0.536	123485	0	10	123495	0.0000405

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0366	171	170	1.01	0.0000124	1909
Missense in Polyphen		72	79.195	0.90915		862
Synonymous	0.778	71	79.8	0.889	0.00000566	707
Loss of Function	1.76	1	5.41	0.185	2.94e-7	71

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000643	0.0000643
Ashkenazi Jewish	0.00	0.00
East Asian	0.000277	0.000277
Finnish	0.0000467	0.0000467
European (Non-Finnish)	0.0000180	0.0000180
Middle Eastern	0.000277	0.000277
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 heparan sulfate. 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:15303968}.
• Pathway: 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: 0.114

Haploinsufficiency Scores

• pHI: 0.0573
• hipred: N
• hipred_score: 0.318
• ghis: 0.474

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.168

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Hs3st6

Gene ontology

• Biological process: blastocyst hatching;glycosaminoglycan biosynthetic process;heparan sulfate proteoglycan biosynthetic process
• Cellular component: Golgi membrane;integral component of membrane
• Molecular function: [heparan sulfate]-glucosamine 3-sulfotransferase 1 activity;heparan sulfate sulfotransferase activity