HS3ST4

heparan sulfate-glucosamine 3-sulfotransferase 4, the group of Sulfotransferases, membrane bound|MicroRNA protein coding host genes

Basic information

Region (hg38): 16:25691958-26137685

Links

ENSG00000182601 ∙ NCBI:9951 ∙ OMIM:604059 ∙ HGNC:5200 ∙ Uniprot:Q9Y661 ∙ 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 HS3ST4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HS3ST4 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			24			24
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	0

Variants in HS3ST4

This is a list of pathogenic ClinVar variants found in the HS3ST4 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-25692425-G-A		not specified	Uncertain significance (Mar 20, 2024)
16-25692464-C-T		not specified	Uncertain significance (Apr 08, 2024)
16-25692652-C-T		not specified	Uncertain significance (Sep 14, 2022)
16-25692653-C-T		not specified	Uncertain significance (Dec 16, 2023)
16-25692667-C-G		not specified	Uncertain significance (Mar 02, 2023)
16-25692688-C-T		not specified	Uncertain significance (Oct 06, 2021)
16-25692706-C-T		not specified	Uncertain significance (Nov 22, 2023)
16-25692737-G-A		not specified	Uncertain significance (Mar 06, 2023)
16-25692738-C-A		not specified	Uncertain significance (Jan 26, 2023)
16-25692758-C-T		not specified	Uncertain significance (Dec 08, 2023)
16-25692760-C-G		not specified	Uncertain significance (Dec 15, 2023)
16-25692803-C-G		not specified	Uncertain significance (Mar 27, 2023)
16-25692845-C-T		not specified	Uncertain significance (Jul 12, 2022)
16-25692864-G-T		not specified	Uncertain significance (Mar 02, 2023)
16-25692868-A-T		not specified	Uncertain significance (Oct 12, 2022)
16-25692876-G-T		not specified	Uncertain significance (Dec 12, 2023)
16-25692886-C-T		not specified	Uncertain significance (Apr 04, 2024)
16-25692887-C-A		not specified	Uncertain significance (May 02, 2024)
16-25692908-C-T		not specified	Uncertain significance (Sep 22, 2022)
16-25692921-C-A		not specified	Uncertain significance (Aug 15, 2023)
16-25692921-C-G		not specified	Uncertain significance (Jun 16, 2024)
16-25692953-G-A		not specified	Uncertain significance (Jan 23, 2024)
16-25693099-G-A		not specified	Uncertain significance (Dec 21, 2023)
16-25693117-G-T		not specified	Uncertain significance (May 26, 2023)
16-26135748-G-A		not specified	Uncertain significance (Feb 21, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HS3ST4	protein_coding	protein_coding	ENST00000331351	2	445663

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.796	0.203	124718	0	3	124721	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.871	158	192	0.823	0.0000101	2881
Missense in Polyphen		65	102.07	0.63682		1273
Synonymous	-1.43	96	79.8	1.20	0.00000447	964
Loss of Function	2.57	1	9.61	0.104	5.56e-7	135

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000178	0.0000177
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. Unlike 3-OST-1, does not convert non- anticoagulant heparan sulfate to anticoagulant heparan sulfate (By similarity). {ECO:0000250}.
• 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)

Haploinsufficiency Scores

• pHI: 0.164
• hipred: Y
• hipred_score: 0.634
• ghis: 0.405

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0447

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hs3st4

Gene ontology

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