CHSY1

chondroitin sulfate synthase 1, the group of Beta 4-glycosyltransferases|Beta 3-glycosyltransferases

Basic information

Region (hg38): 15:101175727-101252048

Links

ENSG00000131873

∙ NCBI:22856 ∙ OMIM:608183 ∙ HGNC:17198 ∙ Uniprot:Q86X52 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

temtamy preaxial brachydactyly syndrome (Definitive), mode of inheritance: AR
temtamy preaxial brachydactyly syndrome (Strong), mode of inheritance: AR
temtamy preaxial brachydactyly syndrome (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Temtamy preaxial brachydactyly syndrome	AR	Audiologic/Otolaryngologic	Early recognition and treatment of hearing impairment may improve outcomes, including speech and language development	Audiologic/Otolaryngologic; Craniofacial; Dental; Musculoskeletal; Neurologic; Ophthalmologic	9823490; 21129728; 19952732; 21129727

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CHSY1 gene.

Temtamy_preaxial_brachydactyly_syndrome (163 variants)
Inborn_genetic_diseases (119 variants)
not_provided (52 variants)
CHSY1-related_disorder (9 variants)
not_specified (7 variants)
Hearing_impairment (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHSY1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000014918.5. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	65 clinvar	10 clinvar	77
missense	1 clinvar		168 clinvar	6 clinvar	1 clinvar	176
nonsense	2 clinvar					2
start loss						0
frameshift	2 clinvar					2
splice donor/acceptor (+/-2bp)						0
Total	5	0	170	71	11

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHSY1	protein_coding	protein_coding	ENST00000254190	3	76210

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.708	0.292	125723	0	25	125748	0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.831	376	424	0.886	0.0000250	5269
Missense in Polyphen		110	168.19	0.65404		2040
Synonymous	-1.96	200	168	1.19	0.0000105	1551
Loss of Function	3.81	5	26.0	0.193	0.00000153	310

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000501	0.000492
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000546	0.0000544
Finnish	0.0000930	0.0000924
European (Non-Finnish)	0.0000970	0.0000967
Middle Eastern	0.0000546	0.0000544
South Asian	0.0000654	0.0000653
Other	0.000164	0.000163

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. Involved in the negative control of osteogenesis likely through the modulation of NOTCH signaling. {ECO:0000269|PubMed:11514575, ECO:0000269|PubMed:21129727}.;
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: 0.113

Intolerance Scores

loftool: 0.117
rvis_EVS: -0.77
rvis_percentile_EVS: 13.15

Haploinsufficiency Scores

pHI: 0.377
hipred: Y
hipred_score: 0.580
ghis: 0.528

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.188

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Chsy1
Phenotype: limbs/digits/tail phenotype; vision/eye phenotype; immune system phenotype; skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype; craniofacial phenotype;

Zebrafish Information Network

Gene name: chsy1
Affected structure: optic furrow
Phenotype tag: abnormal
Phenotype quality: open

Gene ontology

Biological process: chondrocyte development;proximal/distal pattern formation;chondroitin sulfate biosynthetic process;negative regulation of ossification;response to nutrient levels;positive regulation of smoothened signaling pathway;sulfation;bone morphogenesis
Cellular component: Golgi membrane;extracellular region;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