CHST10

carbohydrate sulfotransferase 10, the group of Sulfotransferases, membrane bound

Basic information

Region (hg38): 2:100391860-100417668

Links

ENSG00000115526 ∙ NCBI:9486 ∙ OMIM:606376 ∙ HGNC:19650 ∙ Uniprot:O43529 ∙ 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 CHST10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHST10 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			30	1		31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	1	0

Variants in CHST10

This is a list of pathogenic ClinVar variants found in the CHST10 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-100393318-C-T		not specified	Uncertain significance (Dec 08, 2021)
2-100393327-C-T		not specified	Uncertain significance (Jul 11, 2023)
2-100393408-A-G		not specified	Uncertain significance (Oct 03, 2022)
2-100393414-T-A		not specified	Uncertain significance (May 26, 2024)
2-100393415-G-A		not specified	Uncertain significance (Aug 02, 2021)
2-100393489-A-G		not specified	Uncertain significance (Sep 22, 2023)
2-100393583-C-T		not specified	Uncertain significance (May 13, 2024)
2-100393592-G-A		not specified	Uncertain significance (Nov 18, 2022)
2-100393621-G-A		not specified	Uncertain significance (Feb 01, 2023)
2-100393633-T-C		not specified	Uncertain significance (Jul 26, 2024)
2-100393654-A-G		not specified	Uncertain significance (Jun 11, 2021)
2-100393655-T-C		not specified	Uncertain significance (Dec 27, 2023)
2-100393694-G-A		not specified	Uncertain significance (Nov 29, 2023)
2-100393729-A-G		not specified	Uncertain significance (Aug 27, 2024)
2-100393748-C-G		not specified	Uncertain significance (Aug 17, 2022)
2-100393759-A-T		not specified	Uncertain significance (Sep 14, 2022)
2-100395546-G-A		not specified	Uncertain significance (Nov 10, 2024)
2-100395559-C-G			Uncertain significance (-)
2-100395579-C-T		not specified	Uncertain significance (Oct 12, 2024)
2-100395585-C-T		not specified	Uncertain significance (Jul 06, 2021)
2-100397925-A-C		not specified	Uncertain significance (Jun 11, 2021)
2-100398025-G-A		not specified	Uncertain significance (Oct 12, 2021)
2-100398037-G-C		not specified	Uncertain significance (Dec 10, 2024)
2-100398042-T-C		not specified	Likely benign (Jun 24, 2022)
2-100398054-T-C		not specified	Uncertain significance (Oct 26, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHST10	protein_coding	protein_coding	ENST00000264249	5	25792

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000914	0.941	125724	0	24	125748	0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.983	168	208	0.808	0.0000126	2369
Missense in Polyphen		36	48.368	0.7443		566
Synonymous	0.227	79	81.6	0.968	0.00000532	657
Loss of Function	1.72	9	16.5	0.544	0.00000106	169

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000333	0.000333
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000879	0.0000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.000131	0.000131
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the transfer of sulfate to position 3 of terminal glucuronic acid of both protein- and lipid-linked oligosaccharides. Participates in biosynthesis of HNK-1 carbohydrate structure, a sulfated glucuronyl-lactosaminyl residue carried by many neural recognition molecules, which is involved in cell interactions during ontogenetic development and in synaptic plasticity in the adult. May be indirectly involved in synapse plasticity of the hippocampus, via its role in HNK-1 biosynthesis. {ECO:0000269|PubMed:9478973}.
• Pathway: Mannose type O-glycan biosynthesis - Homo sapiens (human);Metapathway biotransformation Phase I and II;Post-translational protein modification;Reactions specific to the complex N-glycan synthesis pathway;N-glycan antennae elongation in the medial/trans-Golgi;Metabolism of proteins;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation (Consensus)

Recessive Scores

• pRec: 0.119

Intolerance Scores

• loftool: 0.593
• rvis_EVS: 0.53
• rvis_percentile_EVS: 80.88

Haploinsufficiency Scores

• pHI: 0.107
• hipred: N
• hipred_score: 0.379
• ghis: 0.481

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0144

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Chst10
• Phenotype: reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); homeostasis/metabolism phenotype

Gene ontology

• Biological process: cell adhesion;carbohydrate biosynthetic process
• Cellular component: Golgi membrane;Golgi apparatus;membrane;integral component of membrane
• Molecular function: sulfotransferase activity;HNK-1 sulfotransferase activity