HS6ST3

heparan sulfate 6-O-sulfotransferase 3, the group of Sulfotransferases, membrane bound|MicroRNA protein coding host genes

Basic information

Region (hg38): 13:96090106-96839562

Links

ENSG00000185352 ∙ NCBI:266722 ∙ OMIM:609401 ∙ HGNC:19134 ∙ Uniprot:Q8IZP7 ∙ 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 HS6ST3 gene.

• Inborn genetic diseases (26 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HS6ST3 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				1		1
missense			26	1		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	2	0

Variants in HS6ST3

This is a list of pathogenic ClinVar variants found in the HS6ST3 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-96090923-A-C		not specified	Uncertain significance (Sep 17, 2021)
13-96090987-G-T		not specified	Uncertain significance (Mar 06, 2023)
13-96090993-G-C		not specified	Uncertain significance (Jun 06, 2023)
13-96090995-G-A		not specified	Uncertain significance (Aug 09, 2021)
13-96091011-C-T		not specified	Uncertain significance (Jul 14, 2022)
13-96091043-C-A		not specified	Uncertain significance (Jul 12, 2022)
13-96091052-G-A		not specified	Uncertain significance (Feb 08, 2023)
13-96091082-C-T		not specified	Uncertain significance (May 05, 2022)
13-96091091-G-C		not specified	Uncertain significance (Mar 07, 2024)
13-96091100-G-C		not specified	Uncertain significance (Sep 01, 2021)
13-96091101-A-C		not specified	Uncertain significance (Sep 01, 2021)
13-96091102-G-C		not specified	Uncertain significance (Sep 01, 2021)
13-96091104-G-T		not specified	Uncertain significance (Jun 11, 2021)
13-96091107-C-G		not specified	Uncertain significance (Jan 23, 2024)
13-96091110-G-A		not specified	Uncertain significance (Aug 14, 2023)
13-96091191-C-T		not specified	Uncertain significance (Mar 04, 2024)
13-96091266-C-T		not specified	Uncertain significance (Feb 06, 2024)
13-96091269-G-A		not specified	Uncertain significance (May 04, 2022)
13-96091274-G-A		not specified	Uncertain significance (May 25, 2022)
13-96091377-A-G		not specified	Uncertain significance (May 17, 2023)
13-96091395-A-G		not specified	Uncertain significance (Sep 14, 2023)
13-96091403-C-G		not specified	Uncertain significance (Sep 14, 2022)
13-96091476-G-A		not specified	Uncertain significance (May 10, 2023)
13-96091562-C-T		not specified	Uncertain significance (Dec 28, 2023)
13-96832651-G-C		not specified	Uncertain significance (Nov 09, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HS6ST3	protein_coding	protein_coding	ENST00000376705	2	742579

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.990	0.00998	125732	0	14	125746	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.19	207	261	0.793	0.0000144	3087
Missense in Polyphen		73	129.52	0.56363		1384
Synonymous	1.17	89	104	0.854	0.00000535	909
Loss of Function	3.45	0	13.8	0.00	5.95e-7	168

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000890	0.0000879
Middle Eastern	0.00	0.00
South Asian	0.0000328	0.0000327
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: 6-O-sulfation enzyme which catalyzes the transfer of sulfate from 3'-phosphoadenosine 5'-phosphosulfate (PAPS) to position 6 of the N-sulfoglucosamine residue (GlcNS) of 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: 0.115

Intolerance Scores

• loftool: 0.244
• rvis_EVS: -0.11
• rvis_percentile_EVS: 45.26

Haploinsufficiency Scores

• pHI: 0.598
• hipred: Y
• hipred_score: 0.715
• ghis: 0.528

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0877

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hs6st3

Gene ontology

• Biological process: heparan sulfate proteoglycan biosynthetic process, enzymatic modification
• Cellular component: integral component of membrane
• Molecular function: heparan sulfate 6-O-sulfotransferase activity