CHST1

carbohydrate sulfotransferase 1, the group of Sulfotransferases, membrane bound

Basic information

Region (hg38): 11:45647689-45665622

Links

ENSG00000175264 ∙ NCBI:8534 ∙ OMIM:603797 ∙ HGNC:1969 ∙ Uniprot:O43916 ∙ 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 CHST1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHST1 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			21			21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	0	0

Variants in CHST1

This is a list of pathogenic ClinVar variants found in the CHST1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-45649702-G-C		not specified	Uncertain significance (Dec 01, 2022)
11-45649762-C-T		not specified	Uncertain significance (Dec 03, 2021)
11-45649837-G-T		not specified	Uncertain significance (Mar 15, 2024)
11-45649876-C-G		not specified	Uncertain significance (Jul 12, 2023)
11-45649927-G-C		not specified	Uncertain significance (Dec 10, 2024)
11-45650227-C-A		not specified	Uncertain significance (Mar 18, 2024)
11-45650256-G-C		not specified	Uncertain significance (Nov 10, 2022)
11-45650274-C-T		not specified	Uncertain significance (Jan 03, 2024)
11-45650296-C-T		not specified	Uncertain significance (Jun 18, 2021)
11-45650332-G-T		not specified	Uncertain significance (Nov 09, 2021)
11-45650425-C-G		not specified	Uncertain significance (Jan 27, 2025)
11-45650505-T-C		not specified	Uncertain significance (Apr 27, 2023)
11-45650583-C-T		not specified	Uncertain significance (Jul 30, 2024)
11-45650620-G-A		not specified	Uncertain significance (Jun 18, 2024)
11-45650715-C-A		not specified	Uncertain significance (Jun 04, 2024)
11-45650742-G-A		not specified	Uncertain significance (May 24, 2023)
11-45650748-C-T		not specified	Uncertain significance (Jan 15, 2025)
11-45650755-G-T		not specified	Uncertain significance (Jul 30, 2024)
11-45650764-C-T		not specified	Uncertain significance (Jul 15, 2021)
11-45650772-G-A		not specified	Uncertain significance (Apr 20, 2024)
11-45650796-G-A		not specified	Uncertain significance (Mar 29, 2024)
11-45650920-G-C		not specified	Uncertain significance (Oct 29, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHST1	protein_coding	protein_coding	ENST00000308064	1	16746

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.769	0.231	125734	0	10	125744	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.95	161	306	0.525	0.0000238	2613
Missense in Polyphen		57	140.15	0.40672		1218
Synonymous	2.12	118	151	0.781	0.0000128	898
Loss of Function	2.91	2	13.6	0.147	8.45e-7	113

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000617	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000617	0.0000615
Middle Eastern	0.0000545	0.0000544
South Asian	0.0000328	0.0000327
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 galactose (Gal) residues of keratan. Has a preference for sulfating keratan sulfate, but it also transfers sulfate to the unsulfated polymer. The sulfotransferase activity on sialyl LacNAc structures is much higher than the corresponding desialylated substrate, and only internal Gal residues are sulfated. May function in the sulfation of sialyl N- acetyllactosamine oligosaccharide chains attached to glycoproteins. Participates in biosynthesis of selectin ligands. Selectin ligands are present in high endothelial cells (HEVs) and play a central role in lymphocyte homing at sites of inflammation. {ECO:0000269|PubMed:10330415, ECO:0000269|PubMed:10642612}.
• 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;Metabolism (Consensus)

Recessive Scores

• pRec: 0.149

Intolerance Scores

• loftool: 0.0319
• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.75

Haploinsufficiency Scores

• pHI: 0.270
• hipred: Y
• hipred_score: 0.809
• ghis: 0.572

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.746

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Chst1
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype; immune system phenotype; cellular phenotype

Gene ontology

• Biological process: polysaccharide metabolic process;galactose metabolic process;N-acetylglucosamine metabolic process;sulfur compound metabolic process;inflammatory response;keratan sulfate biosynthetic process;keratan sulfate metabolic process
• Cellular component: Golgi membrane;trans-Golgi network;integral component of membrane
• Molecular function: N-acetylglucosamine 6-O-sulfotransferase activity;sulfotransferase activity;keratan sulfotransferase activity