CHSY3

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

Basic information

Region (hg38): 5:129904465-130186634

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.

• not_specified (115 variants)
• not_provided (1 variants)

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. These statistics are base on transcript: NM_000175856.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2		2
missense			112	2		114
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	112	4	0

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