CHST15

carbohydrate sulfotransferase 15, the group of Sulfotransferases, membrane bound

Basic information

Region (hg38): 10:124007668-124093598

Links

ENSG00000182022 ∙ NCBI:51363 ∙ OMIM:608277 ∙ HGNC:18137 ∙ Uniprot:Q7LFX5 ∙ 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 CHST15 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHST15 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					2	2
missense			29	1	1	31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	29	1	4

Variants in CHST15

This is a list of pathogenic ClinVar variants found in the CHST15 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-124010178-C-T		not specified	Uncertain significance (Jul 12, 2023)
10-124010192-G-A		not specified	Uncertain significance (Apr 20, 2024)
10-124010243-A-C		not specified	Uncertain significance (May 29, 2024)
10-124010277-G-T		not specified	Uncertain significance (Apr 06, 2022)
10-124021236-CG-C			Benign (Feb 23, 2021)
10-124021266-T-C		not specified	Uncertain significance (May 16, 2023)
10-124021288-C-T		not specified	Uncertain significance (May 30, 2024)
10-124021293-G-A		not specified	Uncertain significance (Oct 26, 2021)
10-124021296-C-T		not specified	Uncertain significance (Mar 01, 2024)
10-124021341-T-A		not specified	Uncertain significance (Dec 13, 2022)
10-124021363-C-T		not specified	Uncertain significance (Jul 31, 2024)
10-124021369-C-T		not specified	Uncertain significance (Mar 28, 2023)
10-124038592-C-T			Benign (Apr 04, 2018)
10-124038598-C-A		not specified	Uncertain significance (Feb 23, 2023)
10-124038603-C-T		not specified	Uncertain significance (Sep 09, 2024)
10-124038629-G-A		not specified	Uncertain significance (Nov 19, 2024)
10-124038636-C-A		not specified	Uncertain significance (Jun 16, 2024)
10-124042369-T-C		not specified	Uncertain significance (Dec 19, 2022)
10-124042373-C-T		not specified	Uncertain significance (Apr 25, 2022)
10-124042411-T-G		not specified	Uncertain significance (Dec 17, 2021)
10-124042414-C-T		not specified	Uncertain significance (Nov 23, 2024)
10-124042438-C-T		not specified	Uncertain significance (Jul 11, 2023)
10-124044619-C-A		not specified	Uncertain significance (Aug 19, 2024)
10-124044654-T-C		not specified	Uncertain significance (May 30, 2023)
10-124044734-G-C		not specified	Uncertain significance (Nov 11, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHST15	protein_coding	protein_coding	ENST00000346248	7	86023

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000352	0.989	125726	0	22	125748	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.32	280	349	0.802	0.0000222	3735
Missense in Polyphen		48	87.7	0.54732		953
Synonymous	0.387	143	149	0.960	0.0000108	1039
Loss of Function	2.27	11	22.7	0.485	0.00000113	261

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000242	0.000239
Ashkenazi Jewish	0.0000999	0.0000992
East Asian	0.0000587	0.0000544
Finnish	0.0000930	0.0000924
European (Non-Finnish)	0.000108	0.000105
Middle Eastern	0.0000587	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Sulfotransferase that transfers sulfate from 3'- phosphoadenosine 5'-phosphosulfate (PAPS) to the C-6 hydroxyl group of the GalNAc 4-sulfate residue of chondroitin sulfate A and forms chondroitin sulfate E containing GlcA-GalNAc(4,6-SO(4)) repeating units. It also transfers sulfate to a unique non- reducing terminal sequence, GalNAc(4SO4)-GlcA(2SO4)-GalNAc(6SO4), to yield a highly sulfated structure similar to the structure found in thrombomodulin chondroitin sulfate. May also act as a B- cell receptor involved in BCR ligation-mediated early activation that mediate regulatory signals key to B-cell development and/or regulation of B-cell-specific RAG expression; however such results are unclear in vivo. {ECO:0000269|PubMed:11572857, ECO:0000269|PubMed:12874280}.
• Pathway: Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate - Homo sapiens (human);Metabolism of carbohydrates;Chondroitin sulfate biosynthesis;Chondroitin sulfate/dermatan sulfate metabolism;Glycosaminoglycan metabolism;dermatan sulfate biosynthesis (late stages);chondroitin sulfate biosynthesis (late stages);chondroitin sulfate biosynthesis;dermatan sulfate biosynthesis;Metabolism;BCR (Consensus)

Intolerance Scores

• loftool: 0.156
• rvis_EVS: -0.09
• rvis_percentile_EVS: 47.12

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.605
• ghis: 0.526

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.708

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Chst15
• Phenotype: hematopoietic system phenotype; reproductive system phenotype; immune system phenotype

Gene ontology

• Biological process: hexose biosynthetic process;chondroitin sulfate biosynthetic process
• Cellular component: Golgi membrane;integral component of membrane
• Molecular function: 3'-phosphoadenosine 5'-phosphosulfate binding;N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase activity