HS6ST3

protein-coding

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

Gene summary

Heparan sulfate (HS) sulfotransferases, such as HS6ST3, modify HS to generate structures required for interactions between HS and a variety of proteins. These interactions are implicated in proliferation and differentiation, adhesion, migration, inflammation, blood coagulation, and other diverse processes (Habuchi et al., 2000 [PubMed 10644753]).[supplied by OMIM, Mar 2008]

MANE transcript

NM_153456.4

Inheritance

—

ClinVar variants

U:82B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr13:96,090,107-96,839,562

External References & Databases

Ensembl (ENSG00000185352)

Transcript & Mutation Effects

hg38 • Region Span ~749.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to HS6ST3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 80

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_153456.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			81 clinvar	1 clinvar		82
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	82	2	0	84

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 3 of 3 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_153456.4	RefSeq	NP_703157.2	2	MANE Select
ENST00000376705.4	Ensembl	ENSP00000365895.2	2	MANE Select
ENST00001131462.1	Ensembl	ENSP00000810696.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

Biological Process

heparan sulfate proteoglycan biosynthetic process, enzymatic modification

Molecular Function

heparan sulfate 6-O-sulfotransferase activity

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000376705
Coding exons: 2
Length: 742579
Individuals with no LoFs: 125732
Homozygous LoFs: 0
Heterozygous LoFs: 14
Defined: 125746
p: 0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.19	207	261	0.793	0.0000144	3087
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000089	0.000088	rare
South Asian	0.000033	0.000033	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

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.;

Recessive Scores

pRec: 0.115

Intolerance Scores

LoFtool: 0.244
RVIS EVS: -0.11
RVIS percentile EVS: 45.26

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0877

Gene Damage Prediction

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