NDST1
N-deacetylase and N-sulfotransferase 1, the group of Sulfotransferases, membrane bound
Basic information
Region (hg38): 5:150485818-150558211
Previous symbols: [ "HSST" ]
Links
Phenotypes
GenCC
Source:
- autosomal recessive non-syndromic intellectual disability (Supportive), mode of inheritance: AR
- intellectual disability, autosomal recessive 46 (Strong), mode of inheritance: AR
- intellectual disability, autosomal recessive 46 (Moderate), mode of inheritance: AR
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Intellectual developmental disorder, autosomal recessive 46 | AR | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Neurologic | 21937992; 25125150 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (133 variants)
- Inborn_genetic_diseases (101 variants)
- not_specified (31 variants)
- Intellectual_disability,_autosomal_recessive_46 (23 variants)
- NDST1-related_disorder (14 variants)
- Intellectual_disability (5 variants)
- EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)
- Cleft_lip/palate (1 variants)
- Global_developmental_delay (1 variants)
- See_cases (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the NDST1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000001543.5. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 62 | 71 | ||||
| missense | 136 | 149 | ||||
| nonsense | 2 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 2 | 3 | 140 | 70 | 8 |
Highest pathogenic variant AF is 0.000043985725
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| NDST1 | protein_coding | protein_coding | ENST00000261797 | 14 | 72393 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.0000451 | 125737 | 0 | 11 | 125748 | 0.0000437 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.92 | 353 | 545 | 0.648 | 0.0000377 | 5778 |
| Missense in Polyphen | 109 | 223.52 | 0.48765 | 2347 | ||
| Synonymous | -0.126 | 247 | 245 | 1.01 | 0.0000183 | 1771 |
| Loss of Function | 5.54 | 3 | 41.5 | 0.0722 | 0.00000237 | 435 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000867 | 0.0000867 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000616 | 0.0000615 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000373 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
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 (PubMed:10758005, PubMed:12634318). Plays a role in determining the extent and pattern of sulfation of heparan sulfate. Compared to other NDST enzymes, its presence is absolutely required. Participates in biosynthesis of heparan sulfate that can ultimately serve as L-selectin ligands, thereby playing a role in inflammatory response (PubMed:10758005, PubMed:12634318). Required for the exosomal release of SDCBP, CD63 and syndecan (PubMed:22660413). {ECO:0000269|PubMed:10758005, ECO:0000269|PubMed:12634318, ECO:0000269|PubMed:22660413}.;
- 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
- 0.185
Intolerance Scores
- loftool
- 0.0415
- rvis_EVS
- -1.75
- rvis_percentile_EVS
- 2.36
Haploinsufficiency Scores
- pHI
- 0.756
- hipred
- Y
- hipred_score
- 0.685
- ghis
- 0.564
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- H
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.500
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ndst1
- Phenotype
- endocrine/exocrine gland phenotype; taste/olfaction phenotype; growth/size/body region phenotype; craniofacial phenotype; muscle phenotype; cellular phenotype; immune system phenotype; homeostasis/metabolism phenotype; liver/biliary system phenotype; respiratory system phenotype; embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); vision/eye phenotype; hearing/vestibular/ear phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); digestive/alimentary phenotype; renal/urinary system phenotype; skeleton phenotype;
Zebrafish Information Network
- Gene name
- ndst1a
- Affected structure
- basihyal cartilage
- Phenotype tag
- abnormal
- Phenotype quality
- decreased size
Gene ontology
- Biological process
- glycosaminoglycan biosynthetic process;protein sulfation;inflammatory response;heparan sulfate proteoglycan biosynthetic process;heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process;heparin biosynthetic process
- Cellular component
- Golgi membrane;Golgi apparatus;integral component of membrane
- Molecular function
- protein binding;[heparan sulfate]-glucosamine N-sulfotransferase activity;deacetylase activity;heparan sulfate sulfotransferase activity;heparan sulfate N-acetylglucosaminyltransferase activity;N-acetylglucosamine deacetylase activity