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.

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.

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						0
missense			62	3		65
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	62	3	0

Variants in NDST2

This is a list of pathogenic ClinVar variants found in the NDST2 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-73802456-C-T		not specified	Uncertain significance (Jul 09, 2021)
10-73802471-G-T		not specified	Uncertain significance (Aug 12, 2021)
10-73802483-G-A		not specified	Uncertain significance (Feb 28, 2023)
10-73802498-C-T		not specified	Uncertain significance (May 14, 2024)
10-73802523-C-A		not specified	Uncertain significance (Oct 06, 2021)
10-73802572-C-T		not specified	Uncertain significance (Jun 28, 2022)
10-73802684-A-G		not specified	Uncertain significance (Nov 28, 2023)
10-73802707-G-C		not specified	Uncertain significance (Nov 10, 2024)
10-73802711-C-T		not specified	Uncertain significance (Oct 12, 2024)
10-73802717-A-C		not specified	Uncertain significance (Jun 16, 2024)
10-73802723-C-A		not specified	Uncertain significance (Aug 15, 2023)
10-73802735-C-T		not specified	Uncertain significance (Nov 21, 2024)
10-73802773-A-C		not specified	Uncertain significance (Dec 18, 2023)
10-73802976-G-A		not specified	Uncertain significance (May 24, 2023)
10-73802981-C-T		not specified	Uncertain significance (Jul 31, 2023)
10-73803033-T-G		not specified	Uncertain significance (Mar 14, 2023)
10-73803218-G-A		not specified	Uncertain significance (Jul 25, 2023)
10-73803310-T-C		not specified	Uncertain significance (Jul 14, 2024)
10-73803323-A-G		not specified	Uncertain significance (Oct 12, 2021)
10-73803334-A-G		not specified	Uncertain significance (Feb 07, 2023)
10-73803612-G-A		not specified	Uncertain significance (Dec 15, 2022)
10-73803683-G-T		not specified	Uncertain significance (Jun 13, 2023)
10-73803978-C-T		not specified	Uncertain significance (Sep 06, 2022)
10-73804791-C-T		not specified	Uncertain significance (Sep 20, 2023)
10-73805613-G-A		not specified	Uncertain significance (Jan 22, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NDST2	protein_coding	protein_coding	ENST00000309979	13	9921

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.128	0.872	125702	0	46	125748	0.000183

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.55	437	539	0.811	0.0000342	5732
Missense in Polyphen		159	237.93	0.66825		2684
Synonymous	0.311	195	201	0.972	0.0000106	1853
Loss of Function	4.44	10	40.5	0.247	0.00000234	412

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000485	0.000485
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.000231	0.000185
European (Non-Finnish)	0.000185	0.000176
Middle Eastern	0.000272	0.000272
South Asian	0.000229	0.000229
Other	0.00	0.00

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

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

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