NDST3

N-deacetylase and N-sulfotransferase 3, the group of Sulfotransferases, membrane bound

Basic information

Region (hg38): 4:118033618-118258634

Links

ENSG00000164100 ∙ NCBI:9348 ∙ OMIM:603950 ∙ HGNC:7682 ∙ Uniprot:O95803 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NDST3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NDST3 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			31			31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	0	0

Variants in NDST3

This is a list of pathogenic ClinVar variants found in the NDST3 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-118053938-C-G		not specified	Uncertain significance (Sep 25, 2023)
4-118053947-A-G		not specified	Uncertain significance (Jan 06, 2023)
4-118053981-T-G		not specified	Uncertain significance (Jan 08, 2024)
4-118053984-G-T		not specified	Uncertain significance (Jun 12, 2023)
4-118054074-T-C		not specified	Uncertain significance (Nov 10, 2024)
4-118054354-C-A		not specified	Uncertain significance (Feb 27, 2023)
4-118054431-G-A		not specified	Uncertain significance (May 20, 2024)
4-118054461-T-C		not specified	Uncertain significance (Apr 08, 2022)
4-118054470-A-C		not specified	Uncertain significance (Mar 07, 2023)
4-118054567-C-A		not specified	Uncertain significance (Nov 28, 2024)
4-118054661-G-A		not specified	Uncertain significance (Jan 24, 2024)
4-118054791-G-C		not specified	Uncertain significance (Nov 17, 2023)
4-118054794-A-G		not specified	Uncertain significance (Jun 27, 2022)
4-118054798-G-T		not specified	Uncertain significance (Jun 07, 2024)
4-118054829-G-A		not specified	Uncertain significance (Nov 14, 2024)
4-118054850-G-T		not specified	Uncertain significance (Jun 02, 2023)
4-118105093-T-C		not specified	Uncertain significance (Apr 26, 2023)
4-118114853-G-A		not specified	Uncertain significance (Dec 27, 2023)
4-118114911-A-G		not specified	Uncertain significance (Jan 23, 2024)
4-118138060-G-A		not specified	Uncertain significance (Mar 11, 2022)
4-118138192-C-G		not specified	Uncertain significance (Apr 21, 2022)
4-118138210-C-T		not specified	Uncertain significance (Mar 13, 2023)
4-118138219-T-G		not specified	Uncertain significance (Oct 01, 2024)
4-118138220-T-G		not specified	Uncertain significance (Oct 01, 2024)
4-118138221-T-G		not specified	Uncertain significance (Oct 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NDST3	protein_coding	protein_coding	ENST00000296499	13	225031

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000107	1.00	125719	0	29	125748	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.59	300	456	0.659	0.0000222	5776
Missense in Polyphen		98	185.81	0.52742		2452
Synonymous	0.151	162	164	0.985	0.00000837	1624
Loss of Function	3.67	16	41.5	0.386	0.00000213	503

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000219	0.000214
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000187	0.000185
Middle Eastern	0.000109	0.000109
South Asian	0.0000327	0.0000327
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. Has high deacetylase activity but low sulfotransferase activity. {ECO:0000269|PubMed:9915799}.
• 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: 0.120

Intolerance Scores

• loftool: 0.567
• rvis_EVS: -1
• rvis_percentile_EVS: 8.47

Haploinsufficiency Scores

• pHI: 0.353
• hipred: Y
• hipred_score: 0.640
• ghis: 0.599

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.292

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ndst3
• Phenotype: immune system phenotype; skeleton 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; vision/eye phenotype; normal 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; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cellular phenotype; homeostasis/metabolism phenotype; craniofacial phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: heparan sulfate proteoglycan biosynthetic process;heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process;heparin biosynthetic process
• Cellular component: Golgi membrane;cellular_component;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