NDST4

N-deacetylase and N-sulfotransferase 4, the group of Sulfotransferases, membrane bound

Basic information

Region (hg38): 4:114827762-115113876

Links

ENSG00000138653 ∙ NCBI:64579 ∙ OMIM:615039 ∙ HGNC:20779 ∙ Uniprot:Q9H3R1 ∙ 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 NDST4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NDST4 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				1		1
missense			42	2		44
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	43	3	0

Variants in NDST4

This is a list of pathogenic ClinVar variants found in the NDST4 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-114827915-A-C		not specified	Uncertain significance (Dec 21, 2023)
4-114827928-G-A		not specified	Uncertain significance (Jan 19, 2022)
4-114829815-C-T		not specified	Uncertain significance (Jun 10, 2024)
4-114829846-T-C		not specified	Uncertain significance (Mar 23, 2023)
4-114833675-G-A		not specified	Uncertain significance (Mar 07, 2024)
4-114839397-G-T		not specified	Uncertain significance (Nov 21, 2022)
4-114839431-C-T		not specified	Uncertain significance (Jan 04, 2022)
4-114839484-C-T		not specified	Uncertain significance (Aug 02, 2021)
4-114839488-T-C		not specified	Likely benign (Jul 09, 2021)
4-114845861-G-A		not specified	Uncertain significance (Jan 23, 2024)
4-114845863-A-G		not specified	Uncertain significance (Dec 01, 2022)
4-114845873-T-A		not specified	Uncertain significance (May 24, 2023)
4-114845897-C-A		not specified	Uncertain significance (May 17, 2023)
4-114845903-G-A			Uncertain significance (Jan 17, 2019)
4-114848219-C-G		not specified	Uncertain significance (Jan 26, 2022)
4-114848282-G-A		not specified	Uncertain significance (Dec 13, 2022)
4-114848294-T-C		not specified	Uncertain significance (Jul 12, 2022)
4-114848302-G-C		not specified	Uncertain significance (Jun 22, 2023)
4-114848322-A-G			Likely benign (Oct 01, 2022)
4-114848326-A-G		not specified	Uncertain significance (Mar 07, 2024)
4-114848329-G-A		not specified	Uncertain significance (Apr 05, 2023)
4-114870797-A-C		not specified	Uncertain significance (Dec 09, 2023)
4-114870908-G-A		not specified	Uncertain significance (Jan 16, 2024)
4-114935312-C-T		not specified	Uncertain significance (May 29, 2024)
4-114935333-A-T		not specified	Uncertain significance (May 31, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NDST4	protein_coding	protein_coding	ENST00000264363	13	286114

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.34e-8	1.00	125702	0	46	125748	0.000183

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.09	380	445	0.855	0.0000215	5708
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000328	0.000327
Ashkenazi Jewish	0.0000998	0.0000992
East Asian	0.000109	0.000109
Finnish	0.0000927	0.0000924
European (Non-Finnish)	0.000168	0.000158
Middle Eastern	0.000109	0.000109
South Asian	0.000413	0.000392
Other	0.000328	0.000326

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 low deacetylase activity but high sulfotransferase activity (By similarity). {ECO:0000250}.
• 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: 0.104

Intolerance Scores

• loftool: 0.634
• rvis_EVS: -0.04
• rvis_percentile_EVS: 50.5

Haploinsufficiency Scores

• pHI: 0.501
• hipred: Y
• hipred_score: 0.697
• ghis: 0.398

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.210

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ndst4
• Phenotype: cellular phenotype; endocrine/exocrine gland phenotype; digestive/alimentary 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;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