CHST7

carbohydrate sulfotransferase 7, the group of Sulfotransferases, membrane bound

Basic information

Region (hg38): X:46573765-46598496

Links

ENSG00000147119 ∙ NCBI:56548 ∙ OMIM:300375 ∙ HGNC:13817 ∙ Uniprot:Q9NS84 ∙ 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 CHST7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHST7 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				3	2	5
missense			23			23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	3	2

Variants in CHST7

This is a list of pathogenic ClinVar variants found in the CHST7 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-46573956-C-G		not specified	Uncertain significance (Jan 17, 2025)
X-46574001-G-A		not specified	Uncertain significance (Sep 11, 2024)
X-46574001-G-C		not specified	Uncertain significance (Nov 21, 2023)
X-46574014-T-C		not specified	Uncertain significance (May 15, 2024)
X-46574022-G-A		not specified	Uncertain significance (Sep 14, 2022)
X-46574068-C-T		not specified	Uncertain significance (Mar 06, 2025)
X-46574122-A-C		not specified	Uncertain significance (Oct 29, 2021)
X-46574146-G-A		not specified	Uncertain significance (Jun 25, 2024)
X-46574375-C-A		not specified	Uncertain significance (Nov 13, 2023)
X-46574445-G-A		not specified	Uncertain significance (Mar 14, 2024)
X-46574452-C-T		not specified	Uncertain significance (Jun 18, 2024)
X-46574476-C-G		not specified	Uncertain significance (Jan 21, 2025)
X-46574487-A-G		not specified	Uncertain significance (Dec 12, 2023)
X-46574493-A-T		not specified	Uncertain significance (Apr 25, 2022)
X-46574585-C-T			Benign (May 25, 2018)
X-46574729-T-C			Benign (May 30, 2018)
X-46574809-G-T			Uncertain significance (Jun 01, 2023)
X-46574889-G-C		not specified	Uncertain significance (Sep 01, 2021)
X-46574898-C-T		not specified	Uncertain significance (Feb 08, 2025)
X-46574924-G-T			Likely benign (Mar 01, 2023)
X-46574934-C-A		not specified	Uncertain significance (Dec 11, 2023)
X-46574940-G-A		not specified	Uncertain significance (Oct 13, 2023)
X-46574991-C-A		not specified	Uncertain significance (Mar 27, 2023)
X-46575012-G-C		not specified	Uncertain significance (Mar 15, 2024)
X-46575069-C-T		not specified	Conflicting classifications of pathogenicity (Aug 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHST7	protein_coding	protein_coding	ENST00000276055	1	24625

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0687	0.878	124944	1	1	124946	0.00000800

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.94	97	168	0.579	0.0000114	2991
Missense in Polyphen		35	75.476	0.46373		1400
Synonymous	0.219	79	81.5	0.969	0.00000566	1113
Loss of Function	1.63	3	7.97	0.377	5.12e-7	128

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.000109	0.0000654
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. Preferentially acts on mannose-linked GlcNAc. Also able to catalyze the transfer of sulfate to position 6 of the N- acetylgalactosamine (GalNAc) residue of chondroitin. Also acts on core 2 mucin-type oligosaccharide and N-acetyllactosamine oligomer with a lower efficiency. Has weak or no activity toward keratan sulfate and oligosaccharides containing the Galbeta1-4GlcNAc. Catalyzes 6-O-sulfation of beta-benzyl GlcNAc but not alpha- or beta-benzyl GalNAc. {ECO:0000269|PubMed:10781596, ECO:0000269|PubMed:10913333, ECO:0000269|PubMed:10956661}.
• Pathway: Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate - Homo sapiens (human);Metapathway biotransformation Phase I and II;Metabolism of carbohydrates;Chondroitin sulfate biosynthesis;Chondroitin sulfate/dermatan sulfate metabolism;Glycosaminoglycan metabolism;chondroitin sulfate biosynthesis (late stages);Proteoglycan biosynthesis;chondroitin sulfate biosynthesis;Metabolism (Consensus)

Recessive Scores

• pRec: 0.142

Haploinsufficiency Scores

• pHI: 0.532
• hipred: Y
• hipred_score: 0.530
• ghis: 0.430

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Chst7

Gene ontology

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