GeneBe

NDST2

N-deacetylase and N-sulfotransferase 2, the group of Sulfotransferases, membrane bound

Basic information

Region (hg38): 10:73801911-73811798

Links

ENSG00000166507 ∙ NCBI:8509 ∙ OMIM:603268 ∙ HGNC:7681 ∙ Uniprot:P52849 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • schizophrenia (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NDST2 gene.

  • not_specified (128 variants)
  • Anophthalmia-microphthalmia_syndrome (2 variants)
  • not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NDST2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003635.4. 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.

EffectPLPVUSLBBSum
synonymous
0
missense
126
clinvar
4
clinvar
 130
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 126 4 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
NDST2protein_codingprotein_codingENST00000309979 139921
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.1280.8721257020461257480.000183
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.554375390.8110.00003425732
Missense in Polyphen159237.930.668252684
Synonymous0.3111952010.9720.00001061853
Loss of Function4.441040.50.2470.00000234412

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0004850.000485
Ashkenazi Jewish0.000.00
East Asian0.0002720.000272
Finnish0.0002310.000185
European (Non-Finnish)0.0001850.000176
Middle Eastern0.0002720.000272
South Asian0.0002290.000229
Other0.000.00

dbNSFP

Source: dbNSFP

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. Plays a role in determining the extent and pattern of sulfation of heparan sulfate. Required for the exosomal release of SDCBP, CD63 and syndecan (PubMed:22660413). {ECO:0000269|PubMed:10758005, ECO:0000269|PubMed:12634318, ECO:0000269|PubMed:16343444, 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
0.138

Intolerance Scores

loftool
0.360
rvis_EVS
-1.7
rvis_percentile_EVS
2.52

Haploinsufficiency Scores

pHI
0.669
hipred
N
hipred_score
0.433
ghis
0.583

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.195

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Ndst2
Phenotype
hematopoietic system 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); vision/eye phenotype; skeleton phenotype; immune system phenotype; cellular phenotype; endocrine/exocrine gland phenotype;

Gene ontology

Biological process
glycosaminoglycan biosynthetic process;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
[heparan sulfate]-glucosamine N-sulfotransferase activity;deacetylase activity;heparan sulfate sulfotransferase activity;heparan sulfate N-acetylglucosaminyltransferase activity;N-acetylglucosamine deacetylase activity