CHST2

carbohydrate sulfotransferase 2, the group of Sulfotransferases, membrane bound

Basic information

Region (hg38): 3:143119771-143124014

Links

ENSG00000175040 ∙ NCBI:9435 ∙ OMIM:603798 ∙ HGNC:1970 ∙ Uniprot:Q9Y4C5 ∙ 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 CHST2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHST2 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			13	2		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	2	0

Variants in CHST2

This is a list of pathogenic ClinVar variants found in the CHST2 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-143120970-C-G		not specified	Uncertain significance (Aug 02, 2022)
3-143120979-G-A		not specified	Uncertain significance (May 15, 2024)
3-143121009-C-G		not specified	Uncertain significance (Jun 21, 2023)
3-143121076-A-G		not specified	Likely benign (Sep 01, 2021)
3-143121082-A-C		not specified	Uncertain significance (Apr 08, 2024)
3-143121144-C-T		not specified	Uncertain significance (Dec 19, 2022)
3-143121216-G-C		not specified	Uncertain significance (Sep 01, 2021)
3-143121252-G-T		not specified	Likely benign (Jan 08, 2024)
3-143121297-G-C		not specified	Uncertain significance (Apr 12, 2022)
3-143121534-G-A		not specified	Uncertain significance (Jul 27, 2022)
3-143121693-G-C		not specified	Uncertain significance (Feb 01, 2023)
3-143121898-C-G		not specified	Uncertain significance (Oct 29, 2021)
3-143121937-A-C		not specified	Uncertain significance (Sep 25, 2023)
3-143121976-C-G		not specified	Uncertain significance (Apr 13, 2023)
3-143122072-A-G		not specified	Uncertain significance (Sep 29, 2023)
3-143122119-A-G		not specified	Uncertain significance (Nov 09, 2023)
3-143122192-C-T		not specified	Uncertain significance (Feb 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHST2	protein_coding	protein_coding	ENST00000309575	1	3628

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0180	0.963	125729	0	13	125742	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.14	209	316	0.661	0.0000207	3302
Missense in Polyphen		64	143.69	0.44542		1373
Synonymous	0.529	136	144	0.944	0.00000954	1194
Loss of Function	2.05	5	13.0	0.386	6.39e-7	143

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000557	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000924	0.0000879
Middle Eastern	0.0000557	0.0000544
South Asian	0.0000681	0.0000653
Other	0.00	0.00

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 keratan-like structures on N-linked glycans and within mucin-associated glycans that can 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 and in lymphocyte homing to Peyer patches. Has no activity toward O-linked sugars. Its substrate specificity may be influenced by its subcellular location. Sulfates GlcNAc residues at terminal, non-reducing ends of oligosaccharide chains. {ECO:0000269|PubMed:11042394}.
• Pathway: Glycosaminoglycan biosynthesis - keratan sulfate - Homo sapiens (human);Metapathway biotransformation Phase I and II;Metabolism of carbohydrates;Keratan sulfate biosynthesis;Keratan sulfate/keratin metabolism;Glycosaminoglycan metabolism;chondroitin sulfate biosynthesis (late stages);chondroitin sulfate biosynthesis;Metabolism (Consensus)

Recessive Scores

• pRec: 0.144

Intolerance Scores

• loftool: 0.182
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.45

Haploinsufficiency Scores

• pHI: 0.153
• hipred: Y
• hipred_score: 0.577
• ghis: 0.403

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.319

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Chst2
• Phenotype: cellular phenotype; immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: carbohydrate metabolic process;N-acetylglucosamine metabolic process;sulfur compound metabolic process;inflammatory response;multicellular organism development;keratan sulfate biosynthetic process
• Cellular component: Golgi membrane;Golgi apparatus;trans-Golgi network;integral component of membrane;intrinsic component of Golgi membrane
• Molecular function: N-acetylglucosamine 6-O-sulfotransferase activity;sulfotransferase activity