NDST4
protein-codingN-deacetylase and N-sulfotransferase 4, the group of Sulfotransferases, membrane bound
Gene summary
Predicted to enable deacetylase activity and heparan sulfate N-sulfotransferase activity. Predicted to be involved in heparan sulfate proteoglycan biosynthetic process. Predicted to be located in Golgi membrane. Predicted to be active in Golgi apparatus. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~286.1 kbGenCC 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 NDST4 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_022569.3. 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 | 1 | ||||
| missense | 97 | 4 | 101 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 98 | 5 | 0 | 103 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_072091.1 | 13 | MANE Select | |
| Ensembl | ENSP00000264363.2 | 13 | MANE Select | |
| Ensembl | ENSP00000423218.1 | 9 | Standard | |
| Ensembl | ENSP00000483949.1 | 9 | 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
- heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process
- heparin biosynthetic process
Molecular Function
- [heparan sulfate]-glucosamine N-sulfotransferase activity
- deacetylase activity
- heparan sulfate sulfotransferase activity
- heparan sulfate N-acetylglucosaminyltransferase activity
Cellular Component
- Golgi membrane
- Golgi apparatus
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000264363
- Coding exons
- 13
- Length
- 286114
- Individuals with no LoFs
- 125702
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 46
- Defined
- 125748
- p
- 0.000183
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.09 | 380 | 445 | 0.855 | 0.0000215 | 5708 |
| Missense (PolyPhen) | 163 | 225.58 | 0.72258 | 2913 | ||
| Synonymous | -0.695 | 174 | 163 | 1.07 | 0.00000789 | 1649 |
| Loss of Function | 3.50 | 20 | 45.4 | 0.440 | 0.00000265 | 519 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00012 | 0.00012 | rare |
| Latino/Admixed American | 0.00020 | 0.00020 | rare |
| Ashkenazi Jewish | 0.00010 | 0.000099 | rare |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0.000093 | 0.000092 | rare |
| European (Non-Finnish) | 0.00017 | 0.00016 | rare |
| South Asian | 0.00041 | 0.00039 | rare |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Essential bifunctional enzyme that catalyzes both the N- deacetylation and the N-sulfation of glucosamine (GlcNAc) of the glycosaminoglycan in heparan sulfate. Modifies the GlcNAc-GlcA disaccharide repeating sugar backbone to make N-sulfated heparosan, a prerequisite substrate for later modifications in heparin biosynthesis. Has low deacetylase activity but high sulfotransferase activity (By similarity). {ECO:0000250}.;
Recessive Scores
- pRec
- 0.104
Intolerance Scores
- LoFtool
- 0.634
- RVIS EVS
- -0.04
- RVIS percentile EVS
- 50.5
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.210
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |