CHST4

carbohydrate sulfotransferase 4, the group of Sulfotransferases, membrane bound

Basic information

Region (hg38): 16:71525232-71538748

Links

ENSG00000140835 ∙ NCBI:10164 ∙ ∙ HGNC:1972 ∙ Uniprot:Q8NCG5 ∙ 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 CHST4 gene.

• Inborn genetic diseases (22 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHST4 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			19	3		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	3	0

Variants in CHST4

This is a list of pathogenic ClinVar variants found in the CHST4 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-71536745-T-A		not specified	Uncertain significance (Oct 12, 2022)
16-71536792-C-G		not specified	Likely benign (Nov 09, 2021)
16-71536802-G-A		not specified	Likely benign (Aug 12, 2021)
16-71536810-G-A		not specified	Uncertain significance (Aug 30, 2021)
16-71536869-G-T		not specified	Uncertain significance (Aug 16, 2021)
16-71536909-G-A		not specified	Uncertain significance (Dec 20, 2021)
16-71536993-A-G		not specified	Uncertain significance (Oct 27, 2022)
16-71536999-G-A		not specified	Uncertain significance (Dec 20, 2022)
16-71537044-C-G		not specified	Uncertain significance (May 05, 2023)
16-71537065-C-T		not specified	Uncertain significance (Feb 06, 2023)
16-71537122-C-T		not specified	Uncertain significance (Nov 18, 2022)
16-71537123-G-A		not specified	Likely benign (May 27, 2022)
16-71537146-A-G		not specified	Uncertain significance (Dec 01, 2022)
16-71537146-A-T		not specified	Uncertain significance (Jul 09, 2021)
16-71537176-G-T		not specified	Uncertain significance (Jul 06, 2021)
16-71537272-C-T		not specified	Uncertain significance (Feb 28, 2024)
16-71537299-C-T		not specified	Uncertain significance (Apr 07, 2023)
16-71537318-G-A		not specified	Uncertain significance (Aug 21, 2023)
16-71537324-G-A		not specified	Likely benign (Dec 07, 2023)
16-71537324-G-T		not specified	Uncertain significance (Jun 27, 2022)
16-71537351-G-A		not specified	Uncertain significance (Nov 22, 2023)
16-71537354-G-A		not specified	Likely benign (Dec 13, 2023)
16-71537554-T-C		not specified	Uncertain significance (Jul 25, 2023)
16-71537618-G-T		not specified	Uncertain significance (Jan 29, 2024)
16-71537627-A-G		not specified	Uncertain significance (Mar 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHST4	protein_coding	protein_coding	ENST00000338482	1	13514

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.00e-9	0.0721	125682	0	61	125743	0.000243

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.256	231	242	0.954	0.0000151	2539
Missense in Polyphen		102	109.74	0.92949		1077
Synonymous	0.599	87	94.4	0.922	0.00000551	776
Loss of Function	-0.172	13	12.3	1.05	7.70e-7	107

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00131	0.00131
Ashkenazi Jewish	0.00	0.00
East Asian	0.000381	0.000381
Finnish	0.000376	0.000370
European (Non-Finnish)	0.000141	0.000141
Middle Eastern	0.000381	0.000381
South Asian	0.0000981	0.0000653
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Sulfotransferase that utilizes 3'-phospho-5'-adenylyl sulfate (PAPS) as sulfonate donor to catalyze the transfer of sulfate to position 6 of non-reducing N-acetylglucosamine (GlcNAc) residues within mucin-associated glycans that ultimately serve as SELL ligands. SELL ligands are present in high endothelial cells (HEVs) and play a central role in lymphocyte homing at sites of inflammation. Participates in biosynthesis of the SELL ligand sialyl 6-sulfo Lewis X on receptors SPN/CD43, GLYCAM1 and MADCAM1. Also involved in biosynthesis of SELL ligand recognized by MECA-79 antibody. Plays a central role in lymphocyte trafficking during chronic inflammation. Has a catalytic preference for core 2- branched mucin-type O-glycans. Can use GlcNAcbeta1-6[Galbeta1- 3]GalNAc-pNP (core 2), GlcNAcbeta1-6ManOMe and GlcNAcbeta1-2Man oligosaccharide structures as acceptors. Has also activity toward core 3 of GlcNAcbeta1-3GalNAc-pNP. Its substrate specificity may be influenced by its subcellular location. {ECO:0000269|PubMed:10330415}.
• Pathway: Glycosaminoglycan biosynthesis - keratan sulfate - Homo sapiens (human);Metapathway biotransformation Phase I and II;Post-translational protein modification;Metabolism of proteins;O-linked glycosylation of mucins;O-linked glycosylation (Consensus)

Recessive Scores

• pRec: 0.134

Intolerance Scores

• loftool: 0.151
• rvis_EVS: -0.02
• rvis_percentile_EVS: 52.09

Haploinsufficiency Scores

• pHI: 0.328
• hipred: N
• hipred_score: 0.146
• ghis: 0.369

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.722

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Chst4
• Phenotype: cellular phenotype; immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: carbohydrate metabolic process;N-acetylglucosamine metabolic process;protein sulfation;sulfur compound metabolic process;inflammatory response;immune response;cell adhesion;cell-cell signaling;O-glycan processing
• Cellular component: Golgi membrane;trans-Golgi network;integral component of membrane;intrinsic component of Golgi membrane
• Molecular function: N-acetylglucosamine 6-O-sulfotransferase activity;sulfotransferase activity