CHST13

carbohydrate sulfotransferase 13, the group of Sulfotransferases, membrane bound

Basic information

Region (hg38): 3:126524155-126543291

Links

ENSG00000180767 ∙ NCBI:166012 ∙ OMIM:610124 ∙ HGNC:21755 ∙ Uniprot:Q8NET6 ∙ 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 CHST13 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHST13 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			34			34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	34	0	0

Variants in CHST13

This is a list of pathogenic ClinVar variants found in the CHST13 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-126524348-T-C		not specified	Uncertain significance (Jan 03, 2025)
3-126524367-C-A		not specified	Uncertain significance (Nov 07, 2024)
3-126524375-T-A		not specified	Uncertain significance (Apr 13, 2023)
3-126524427-C-G		not specified	Uncertain significance (Mar 25, 2024)
3-126536323-C-G		not specified	Uncertain significance (Mar 28, 2022)
3-126536336-C-T		not specified	Uncertain significance (Feb 08, 2025)
3-126541737-C-T		not specified	Uncertain significance (Aug 21, 2024)
3-126541767-A-G		not specified	Uncertain significance (Jan 31, 2023)
3-126541842-G-T		not specified	Uncertain significance (Mar 19, 2024)
3-126541846-C-G		not specified	Uncertain significance (Jun 29, 2023)
3-126541887-T-A		not specified	Uncertain significance (Apr 04, 2024)
3-126541905-C-T		not specified	Uncertain significance (Jan 22, 2025)
3-126541929-C-A		not specified	Uncertain significance (May 14, 2024)
3-126541937-G-A		not specified	Uncertain significance (Jan 31, 2023)
3-126541937-G-C		not specified	Uncertain significance (Apr 18, 2024)
3-126541959-G-C		not specified	Uncertain significance (Mar 16, 2022)
3-126541959-G-T		not specified	Uncertain significance (Dec 12, 2024)
3-126542035-C-A		not specified	Uncertain significance (Jan 26, 2022)
3-126542120-C-G		not specified	Uncertain significance (Nov 12, 2021)
3-126542124-C-T		not specified	Uncertain significance (Jan 23, 2024)
3-126542129-A-T		not specified	Uncertain significance (Feb 07, 2025)
3-126542148-G-A		not specified	Uncertain significance (Dec 14, 2023)
3-126542156-G-C		not specified	Uncertain significance (Nov 18, 2022)
3-126542160-G-T		not specified	Uncertain significance (Sep 26, 2024)
3-126542175-T-G		not specified	Uncertain significance (Nov 03, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHST13	protein_coding	protein_coding	ENST00000319340	3	19009

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000121	0.402	125708	0	13	125721	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.25	143	192	0.745	0.0000161	2040
Missense in Polyphen		47	78.674	0.5974		760
Synonymous	2.21	63	89.6	0.703	0.00000749	752
Loss of Function	0.122	6	6.33	0.948	2.69e-7	94

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000337	0.000337
Ashkenazi Jewish	0.00	0.00
East Asian	0.000178	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000188	0.0000176
Middle Eastern	0.000178	0.000163
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the transfer of sulfate to position 4 of the N-acetylgalactosamine (GalNAc) residue of chondroitin. Chondroitin sulfate constitutes the predominant proteoglycan present in cartilage and is distributed on the surfaces of many cells and extracellular matrices. Transfers sulfate to the C4 hydroxyl of beta1,4-linked GalNAc that is substituted with a beta-linked glucuronic acid at the C-3 hydroxyl. No activity toward dermatan.
• 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: 0.113

Haploinsufficiency Scores

• pHI: 0.0941
• hipred: N
• hipred_score: 0.439
• ghis: 0.427

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.955

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Chst13

Gene ontology

• Biological process: carbohydrate biosynthetic process;chondroitin sulfate biosynthetic process
• Cellular component: Golgi membrane;integral component of membrane
• Molecular function: N-acetylgalactosamine 4-O-sulfotransferase activity;chondroitin 4-sulfotransferase activity