CHSY3

chondroitin sulfate synthase 3, the group of Beta 4-glycosyltransferases|Beta 3-glycosyltransferases

Basic information

Region (hg38): 5:129904464-130186634

Links

ENSG00000198108 ∙ NCBI:337876 ∙ OMIM:609963 ∙ HGNC:24293 ∙ Uniprot:Q70JA7 ∙ 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 CHSY3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHSY3 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				1		1
missense			60	2		62
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	60	3	0

Variants in CHSY3

This is a list of pathogenic ClinVar variants found in the CHSY3 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-129904987-C-T		not specified	Uncertain significance (Jul 05, 2023)
5-129904993-C-A		not specified	Uncertain significance (Apr 07, 2022)
5-129905008-A-T		not specified	Uncertain significance (Jun 02, 2024)
5-129905026-C-T		not specified	Likely benign (Oct 26, 2021)
5-129905034-C-G		not specified	Uncertain significance (Feb 10, 2022)
5-129905041-G-C		not specified	Uncertain significance (Nov 30, 2022)
5-129905071-A-G		not specified	Uncertain significance (Aug 13, 2021)
5-129905109-G-A		not specified	Uncertain significance (Jan 18, 2023)
5-129905110-G-A		not specified	Uncertain significance (Apr 30, 2024)
5-129905250-G-A		not specified	Uncertain significance (Oct 26, 2022)
5-129905262-C-T		not specified	Uncertain significance (Aug 26, 2022)
5-129905266-G-C		not specified	Uncertain significance (Dec 19, 2023)
5-129905295-G-C		not specified	Uncertain significance (Aug 02, 2021)
5-129905308-G-A		not specified	Uncertain significance (Feb 10, 2022)
5-129905308-G-C		not specified	Uncertain significance (Aug 16, 2022)
5-129905340-G-C		not specified	Uncertain significance (Jan 04, 2022)
5-129905419-G-A		not specified	Uncertain significance (Aug 12, 2021)
5-129905479-C-G		not specified	Uncertain significance (Jan 03, 2024)
5-129905503-C-G		not specified	Uncertain significance (Jan 23, 2024)
5-129905581-T-C		not specified	Uncertain significance (Dec 21, 2021)
5-129905597-G-T		not specified	Uncertain significance (Mar 25, 2022)
5-129908128-A-T		not specified	Uncertain significance (Feb 12, 2024)
5-129908259-A-G		not specified	Uncertain significance (Oct 06, 2021)
5-129908263-G-T		not specified	Uncertain significance (Feb 06, 2023)
5-129908274-A-G		not specified	Uncertain significance (Nov 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHSY3	protein_coding	protein_coding	ENST00000305031	3	282163

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00284	0.997	125734	0	14	125748	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.839	421	472	0.891	0.0000235	5744
Missense in Polyphen		128	184.37	0.69427		2181
Synonymous	-1.35	205	182	1.13	0.00000900	1722
Loss of Function	3.38	10	30.0	0.334	0.00000154	355

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000530	0.0000527
Middle Eastern	0.000109	0.000109
South Asian	0.0000653	0.0000653
Other	0.000533	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has both beta-1,3-glucuronic acid and beta-1,4-N- acetylgalactosamine transferase activity. Transfers glucuronic acid (GlcUA) from UDP-GlcUA and N-acetylgalactosamine (GalNAc) from UDP-GalNAc to the non-reducing end of the elongating chondroitin polymer. Specific activity is much reduced compared to CHSY1. {ECO:0000269|PubMed:12907687}.
• Pathway: Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate - Homo sapiens (human);Metabolism of carbohydrates;Chondroitin sulfate biosynthesis;Chondroitin sulfate/dermatan sulfate metabolism;Glycosaminoglycan metabolism;chondroitin sulfate biosynthesis (late stages);Proteoglycan biosynthesis;chondroitin sulfate biosynthesis;dermatan sulfate biosynthesis;Metabolism;chondroitin and dermatan biosynthesis (Consensus)

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.330
• rvis_EVS: -0.73
• rvis_percentile_EVS: 14.14

Haploinsufficiency Scores

• pHI: 0.270
• hipred: Y
• hipred_score: 0.614
• ghis: 0.573

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.244

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Chsy3

Gene ontology

• Biological process: chondroitin sulfate biosynthetic process
• Cellular component: Golgi membrane;integral component of membrane;Golgi cisterna membrane
• Molecular function: metal ion binding;glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity;N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity