HS3ST6
protein-codingheparan sulfate-glucosamine 3-sulfotransferase 6, the group of Sulfotransferases, membrane bound
Gene summary
Predicted to enable [heparan sulfate]-glucosamine 3-sulfotransferase activity. Predicted to be involved in heparan sulfate proteoglycan biosynthetic process. Predicted to act upstream of or within blastocyst hatching. Predicted to be located in Golgi membrane. Implicated in hereditary angioedema. [provided by Alliance of Genome Resources, Jul 2025]
- HS3ST5
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~6.9 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0030298
Submitter: PanelApp Australia
Clinical Genomic Database (CGD)
Manifestation: Allergy/Immunology/Infectious
Intervention: Allergy/Immunology/Infectious
Rationale: 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
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to HS3ST6 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001009606.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 5 | 6 | |||
| missense | 1 | 79 | 1 | 81 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 1 | 0 | 80 | 6 | 0 | 87 |
Highest pathogenic variant AF is 0.0000027779822
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001009606.3 | 2 | MANE Select | |
| Ensembl | ENSP00000416741.3 | 2 | MANE Select | |
| RefSeq | XP_011520910.1 | 2 | Standard | |
| RefSeq | XP_011520911.1 | 1 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Metapathway biotransformation Phase I and II
- Metabolism of carbohydrates
- HS-GAG biosynthesis
- Heparan sulfate/heparin (HS-GAG) metabolism
- Glycosaminoglycan metabolism
Biological Process
- blastocyst hatching
- glycosaminoglycan biosynthetic process
- heparan sulfate proteoglycan biosynthetic process
Molecular Function
- [heparan sulfate]-glucosamine 3-sulfotransferase 1 activity
- heparan sulfate sulfotransferase activity
Cellular Component
- Golgi membrane
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000443547
- Coding exons
- 2
- Length
- 6978
- Individuals with no LoFs
- 123485
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 10
- Defined
- 123495
- p
- 0.0000405
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.0366 | 171 | 170 | 1.01 | 0.0000124 | 1909 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000064 | 0.000064 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00028 | 0.00028 | rare |
| Finnish | 0.000047 | 0.000047 | rare |
| European (Non-Finnish) | 0.000018 | 0.000018 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- 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}.;
Recessive Scores
- pRec
- 0.114
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.168
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | High | High | High |
| Primary Immunodeficiency | High | High | High |
| Cancer | High | High | High |