HS3ST3A1

heparan sulfate-glucosamine 3-sulfotransferase 3A1, the group of Sulfotransferases, membrane bound|MicroRNA protein coding host genes

Basic information

Region (hg38): 17:13494031-13601929

Links

ENSG00000153976 ∙ NCBI:9955 ∙ OMIM:604057 ∙ HGNC:5196 ∙ Uniprot:Q9Y663 ∙ 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 HS3ST3A1 gene.

• Inborn genetic diseases (10 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HS3ST3A1 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			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	0

Variants in HS3ST3A1

This is a list of pathogenic ClinVar variants found in the HS3ST3A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-13496280-C-T		not specified	Uncertain significance (Dec 11, 2023)
17-13496289-G-T		not specified	Uncertain significance (Jun 07, 2023)
17-13496297-T-G		not specified	Uncertain significance (Oct 10, 2023)
17-13496319-T-A		not specified	Uncertain significance (Jan 16, 2024)
17-13496388-T-C		not specified	Uncertain significance (Jan 12, 2024)
17-13496553-C-T		not specified	Uncertain significance (Dec 08, 2023)
17-13496574-A-G		not specified	Uncertain significance (Sep 14, 2022)
17-13496598-T-C		not specified	Uncertain significance (Apr 26, 2023)
17-13496637-G-A		not specified	Uncertain significance (Jul 27, 2023)
17-13496708-T-G		not specified	Uncertain significance (Dec 21, 2023)
17-13496727-C-G		not specified	Uncertain significance (Dec 21, 2023)
17-13496745-C-A		not specified	Uncertain significance (Oct 26, 2021)
17-13496748-C-G		not specified	Uncertain significance (Jun 02, 2023)
17-13496817-C-T		Inborn genetic diseases	Uncertain significance (Feb 02, 2022)
17-13600541-C-A		not specified	Uncertain significance (Nov 09, 2021)
17-13600727-C-T		not specified	Uncertain significance (Jul 09, 2021)
17-13600765-C-G		not specified	Uncertain significance (Oct 10, 2023)
17-13600825-G-A		not specified	Uncertain significance (Nov 29, 2023)
17-13600955-C-T		not specified	Uncertain significance (Feb 21, 2024)
17-13600991-G-C		not specified	Uncertain significance (Oct 12, 2021)
17-13601089-G-A		not specified	Uncertain significance (Feb 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HS3ST3A1	protein_coding	protein_coding	ENST00000284110	2	106239

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0136	0.875	125736	0	8	125744	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.420	205	223	0.921	0.0000143	2530
Missense in Polyphen		70	72.747	0.96224		877
Synonymous	0.0706	102	103	0.991	0.00000701	863
Loss of Function	1.32	4	8.05	0.497	3.44e-7	112

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000898	0.0000898
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000495	0.0000440
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. Catalyzes the O-sulfation of glucosamine in IdoUA2S-GlcNS and also in 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. Unlike 3-OST-1, does not convert non- anticoagulant heparan sulfate to anticoagulant heparan sulfate. {ECO:0000269|PubMed:10520990}.
• 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: 0.142

Haploinsufficiency Scores

• pHI: 0.0425
• ghis: 0.401

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0883

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hs3st3a1

Gene ontology

• Biological process: glycosaminoglycan biosynthetic process;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 3 activity;heparan sulfate sulfotransferase activity