HS3ST5

heparan sulfate-glucosamine 3-sulfotransferase 5, the group of Sulfotransferases, membrane bound

Basic information

Region (hg38): 6:114055596-114343023

Links

ENSG00000249853 ∙ NCBI:222537 ∙ OMIM:609407 ∙ HGNC:19419 ∙ Uniprot:Q8IZT8 ∙ 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 HS3ST5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HS3ST5 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			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	0

Variants in HS3ST5

This is a list of pathogenic ClinVar variants found in the HS3ST5 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-114057362-A-C		not specified	Uncertain significance (May 02, 2024)
6-114057402-A-G		not specified	Uncertain significance (Nov 06, 2023)
6-114057435-G-A		not specified	Uncertain significance (Jan 09, 2024)
6-114057583-C-T		not specified	Uncertain significance (Oct 03, 2022)
6-114057609-C-G		not specified	Uncertain significance (Feb 07, 2023)
6-114057766-A-T		not specified	Uncertain significance (May 10, 2024)
6-114057943-C-T		not specified	Uncertain significance (Jul 20, 2021)
6-114058035-T-C		not specified	Uncertain significance (Oct 12, 2021)
6-114058053-C-T		not specified	Uncertain significance (Feb 07, 2023)
6-114058062-T-C		not specified	Uncertain significance (Nov 17, 2023)
6-114058104-C-T		not specified	Uncertain significance (Aug 17, 2022)
6-114058116-A-G		not specified	Uncertain significance (May 06, 2024)
6-114058146-C-T		not specified	Uncertain significance (Oct 20, 2021)
6-114058161-C-T		not specified	Uncertain significance (Feb 12, 2024)
6-114062751-C-A		not specified	Uncertain significance (Apr 04, 2024)
6-114062761-C-T		not specified	Uncertain significance (Mar 21, 2023)
6-114062821-G-T		not specified	Uncertain significance (Feb 21, 2024)
6-114062841-A-G		not specified	Uncertain significance (Aug 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HS3ST5	protein_coding	protein_coding	ENST00000312719	2	287460

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.166	0.821	125688	0	3	125691	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.29	143	194	0.739	0.0000111	2274
Missense in Polyphen		38	70.774	0.53692		896
Synonymous	-0.599	84	77.3	1.09	0.00000439	683
Loss of Function	2.15	3	10.5	0.285	5.17e-7	141

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	0.00	0.00
Other	0.000163	0.000163

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. Also generates GlcUA- GlcNS or IdoUA-GlcNS and IdoUA2S-GlcNH2. 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. {ECO:0000269|PubMed:12138164}.
• Pathway: Glycosaminoglycan biosynthesis - heparan sulfate / heparin - Homo sapiens (human);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

Intolerance Scores

• loftool: 0.131
• rvis_EVS: 0.11
• rvis_percentile_EVS: 61.73

Haploinsufficiency Scores

• pHI: 0.487
• hipred: Y
• hipred_score: 0.558
• ghis: 0.488

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.161

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hs3st5

Gene ontology

• Biological process: glycosaminoglycan biosynthetic process;protein sulfation;heparan sulfate proteoglycan biosynthetic process;heparan sulfate proteoglycan biosynthetic process, enzymatic modification;regulation of viral entry into host cell;negative regulation of coagulation
• Cellular component: Golgi membrane;integral component of membrane
• Molecular function: protein binding;[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity;heparan sulfate sulfotransferase activity;3'-phosphoadenosine 5'-phosphosulfate binding