HS3ST2

heparan sulfate-glucosamine 3-sulfotransferase 2, the group of Sulfotransferases, membrane bound

Basic information

Region (hg38): 16:22814162-22916338

Links

ENSG00000122254 ∙ NCBI:9956 ∙ OMIM:604056 ∙ HGNC:5195 ∙ Uniprot:Q9Y278 ∙ 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 HS3ST2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HS3ST2 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			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	0	0

Variants in HS3ST2

This is a list of pathogenic ClinVar variants found in the HS3ST2 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-22814741-T-C		not specified	Uncertain significance (Aug 13, 2021)
16-22814752-C-G		not specified	Uncertain significance (May 31, 2023)
16-22814795-G-C		not specified	Uncertain significance (Jul 13, 2022)
16-22814846-C-T		not specified	Uncertain significance (Apr 08, 2024)
16-22814881-G-C		not specified	Uncertain significance (Jun 18, 2021)
16-22814920-T-C		not specified	Uncertain significance (Dec 17, 2023)
16-22814998-G-C		not specified	Uncertain significance (Apr 14, 2022)
16-22815016-G-A		not specified	Uncertain significance (Apr 17, 2024)
16-22915158-C-T		not specified	Uncertain significance (Oct 06, 2021)
16-22915185-G-A		not specified	Uncertain significance (Feb 21, 2024)
16-22915291-T-C		not specified	Uncertain significance (Jun 26, 2024)
16-22915392-C-A		not specified	Uncertain significance (Apr 08, 2022)
16-22915413-T-A		not specified	Uncertain significance (Oct 05, 2023)
16-22915536-G-A		not specified	Uncertain significance (Oct 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HS3ST2	protein_coding	protein_coding	ENST00000261374	2	102162

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.100	0.893	125735	0	4	125739	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.30	123	219	0.562	0.0000133	2331
Missense in Polyphen		24	85.44	0.2809		942
Synonymous	-1.47	117	98.5	1.19	0.00000638	783
Loss of Function	2.37	4	13.3	0.300	0.00000107	115

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)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
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 GlcA2S-GlcNS. Unlike 3-OST-1, does not convert non-anticoagulant heparan sulfate to anticoagulant heparan sulfate.
• 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: 0.134

Intolerance Scores

• loftool: 0.169
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.64

Haploinsufficiency Scores

• pHI: 0.404
• hipred: Y
• hipred_score: 0.755
• ghis: 0.405

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.414

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hs3st2
• Phenotype: normal phenotype

Gene ontology

• Biological process: glycosaminoglycan biosynthetic process;circadian rhythm;heparan sulfate proteoglycan biosynthetic process
• Cellular component: Golgi membrane;integral component of membrane
• Molecular function: sulfotransferase activity;[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity;[heparan sulfate]-glucosamine 3-sulfotransferase 2 activity;heparan sulfate sulfotransferase activity