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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 15 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
CHST3
carbohydrate sulfotransferase 3
Chromosome 10 Β· 10q22.1
NCBI Gene: 9469Ensembl: ENSG00000122863.7HGNC: HGNC:1971UniProt: Q7LGC8
45PubMed Papers
21Diseases
0Drugs
57Pathogenic Variants
RESEARCH IMPACT
Variant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
sulfur compound metabolic processchondroitin sulfate proteoglycan biosynthetic processchondroitin 6-sulfotransferase activityN-acetylglucosamine 6-O-sulfotransferase activityspondyloepiphyseal dysplasia with congenital joint dislocationsCHST3-related skeletal dysplasiaBack painosteoarthritis, hip
✦AI Summary

CHST3 encodes a sulfotransferase enzyme that catalyzes sulfation of chondroitin at the 6-position of N-acetylgalactosamine residues using PAPS as a sulfate donor 123. This modification is critical for chondroitin sulfate biosynthesis, the predominant proteoglycan in cartilage and extracellular matrices. CHST3 also sulfates keratan sulfate galactose residues with lower efficiency 2 and may contribute to naive T-lymphocyte maintenance. Biallelic loss-of-function CHST3 variants cause spondyloepiphyseal dysplasia with congenital joint dislocations (CDCJD), a rare skeletal dysplasia characterized by congenital knee and elbow dislocations, short stature, progressive vertebral anomalies, kyphoscoliosis, and joint contractures 4567. Cardiac valve abnormalities and progressive hearing loss are significant clinical manifestations requiring monitoring 78. The c.776T>C mutation shows ethnic clustering in Turkish populations 5, while variants demonstrate geographic diversity across populations 9. Beyond skeletal dysplasia, CHST3 variants have been identified as potential diagnostic genes for osteoporosis and sarcopenia 10, implicating broader roles in bone and muscle metabolism. Genotype-phenotype correlation remains unclear, with both missense and nonmissense mutations producing variable clinical presentations 4.

Sources cited
1
CHST3 catalyzes sulfate transfer to GalNAc residues of chondroitin
PMID: 15215498
2
CHST3 sulfates chondroitin and keratan sulfate; chondroitin sulfate is predominant proteoglycan in cartilage
PMID: 9714738
3
CHST3 catalyzes sulfation of chondroitin using PAPS as sulfate donor
PMID: 9883891
4
CHST3 mutations cause spondyloepiphyseal dysplasia with congenital joint dislocations; progressive joint pain and movement restriction are main features
PMID: 36729370
5
CHST3 mutations cause chondrodysplasia with congenital joint dislocations; c.776T>C is recurrent mutation in Turkish patients
PMID: 32639237
6
CHST3 is critical for chondroitin sulfate sulfation; biallelic variants cause CDCJD with joint dislocations and cardiac abnormalities
PMID: 37876363
7
CHST3 variants cause spondyloepiphyseal dysplasia with cardiac valve involvement and hearing loss; bifid humeral distal ends are diagnostic feature
PMID: 37183573
8
CHST3 encodes chondroitin 6-O-sulfotransferase-1; mutations cause skeletal dysplasia with hearing loss
PMID: 26572954
9
CHST3 identified as potential diagnostic gene for osteoporosis and sarcopenia
PMID: 39747879
10
CHST3 shows haplotype polymorphism diversity across ethnic populations
PMID: 34876832
Disease Associationsβ“˜21
spondyloepiphyseal dysplasia with congenital joint dislocationsOpen Targets
0.82Strong
CHST3-related skeletal dysplasiaOpen Targets
0.72Strong
Back painOpen Targets
0.48Moderate
osteoarthritis, hipOpen Targets
0.47Moderate
vertebral column disorderOpen Targets
0.44Moderate
Larsen syndromeOpen Targets
0.42Moderate
medical procedureOpen Targets
0.40Moderate
total hip arthroplastyOpen Targets
0.39Weak
Low back painOpen Targets
0.39Weak
spinal cord injuryOpen Targets
0.38Weak
vertebral disorderOpen Targets
0.38Weak
musculoskeletal system diseaseOpen Targets
0.38Weak
Intervertebral Disc DisplacementOpen Targets
0.38Weak
Spondyloepiphyseal dysplasia and spondyloepimetaphyseal dysplasiaOpen Targets
0.37Weak
osteoarthritis, kneeOpen Targets
0.33Weak
alcohol drinkingOpen Targets
0.32Weak
osteoarthritisOpen Targets
0.31Weak
vertebral joint diseaseOpen Targets
0.31Weak
lesion of sciatic nerveOpen Targets
0.31Weak
SciaticaOpen Targets
0.31Weak
Spondyloepiphyseal dysplasia with congenital joint dislocationsUniProt
Pathogenic Variants57
NM_004273.5(CHST3):c.475T>A (p.Phe159Ile)Pathogenic
Spondyloepiphyseal dysplasia with congenital joint dislocations|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 159
NM_004273.5(CHST3):c.533dup (p.Ala179fs)Pathogenic
not provided|Spondyloepiphyseal dysplasia with congenital joint dislocations
β˜…β˜…β˜†β˜†2025β†’ Residue 179
NM_004273.5(CHST3):c.375_378dup (p.Ala127fs)Pathogenic
Spondyloepiphyseal dysplasia with congenital joint dislocations|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 127
NM_004273.5(CHST3):c.661C>T (p.Arg221Cys)Pathogenic
Spondyloepiphyseal dysplasia with congenital joint dislocations|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 221
NM_004273.5(CHST3):c.688G>T (p.Glu230Ter)Pathogenic
Spondyloepiphyseal dysplasia with congenital joint dislocations|not provided
β˜…β˜…β˜†β˜†2023β†’ Residue 230
NM_004273.5(CHST3):c.1291dup (p.Ser431fs)Likely pathogenic
Spondyloepiphyseal dysplasia with congenital joint dislocations|not provided
β˜…β˜…β˜†β˜†2023β†’ Residue 431
NM_004273.5(CHST3):c.168_186dup (p.Asn63fs)Likely pathogenic
not provided
β˜…β˜…β˜†β˜†2019β†’ Residue 63
NM_004273.5(CHST3):c.723dup (p.Phe242fs)Pathogenic
Spondyloepiphyseal dysplasia with congenital joint dislocations
β˜…β˜†β˜†β˜†2025β†’ Residue 242
NM_004273.5(CHST3):c.271C>T (p.Gln91Ter)Pathogenic
Spondyloepiphyseal dysplasia with congenital joint dislocations
β˜…β˜†β˜†β˜†2025β†’ Residue 91
NM_004273.5(CHST3):c.855del (p.Leu286fs)Pathogenic
Spondyloepiphyseal dysplasia with congenital joint dislocations
β˜…β˜†β˜†β˜†2025β†’ Residue 286
NM_004273.5(CHST3):c.780del (p.Ala261fs)Likely pathogenic
Spondyloepiphyseal dysplasia with congenital joint dislocations
β˜…β˜†β˜†β˜†2025β†’ Residue 261
NM_004273.5(CHST3):c.802G>T (p.Glu268Ter)Pathogenic
Spondyloepiphyseal dysplasia with congenital joint dislocations
β˜…β˜†β˜†β˜†2025β†’ Residue 268
NM_004273.5(CHST3):c.400C>T (p.His134Tyr)Likely pathogenic
Spondyloepiphyseal dysplasia with congenital joint dislocations
β˜…β˜†β˜†β˜†2025β†’ Residue 134
NM_004273.5(CHST3):c.696dup (p.Val233fs)Pathogenic
Spondyloepiphyseal dysplasia with congenital joint dislocations
β˜…β˜†β˜†β˜†2025β†’ Residue 233
NM_004273.5(CHST3):c.685_686del (p.Cys229fs)Pathogenic
Spondyloepiphyseal dysplasia with congenital joint dislocations
β˜…β˜†β˜†β˜†2025β†’ Residue 229
NM_004273.5(CHST3):c.862G>T (p.Glu288Ter)Likely pathogenic
Spondyloepiphyseal dysplasia with congenital joint dislocations
β˜…β˜†β˜†β˜†2024β†’ Residue 288
NM_004273.5(CHST3):c.757G>A (p.Gly253Ser)Likely pathogenic
Spondyloepiphyseal dysplasia with congenital joint dislocations
β˜…β˜†β˜†β˜†2024β†’ Residue 253
NM_004273.5(CHST3):c.718A>T (p.Lys240Ter)Pathogenic
Spondyloepiphyseal dysplasia with congenital joint dislocations
β˜…β˜†β˜†β˜†2024β†’ Residue 240
NM_004273.5(CHST3):c.58_77dup (p.Leu26_Phe27insTer)Pathogenic
Spondyloepiphyseal dysplasia with congenital joint dislocations
β˜…β˜†β˜†β˜†2024β†’ Residue 26
NM_004273.5(CHST3):c.763del (p.Leu255fs)Pathogenic
Spondyloepiphyseal dysplasia with congenital joint dislocations
β˜…β˜†β˜†β˜†2024β†’ Residue 255
View on ClinVar β†—
Related Genes
CHST7Protein interaction88%CHST12Protein interaction81%CHST13Protein interaction81%CHST6Shared pathway80%CHST5Shared pathway80%CHST15Protein interaction77%
Tissue Expression6 tissues
Ovary
100%
Heart
62%
Brain
35%
Lung
27%
Liver
5%
Bone Marrow
1%
Gene Interaction Network
Click a node to explore
CHST3CHST7CHST12CHST13CHST6CHST5CHST15
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted Β· UniProt Q7LGC8
View on AlphaFold β†—
Constraintβ“˜
LOEUFβ“˜
1.12LoF Tolerant
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.77 [0.54–1.12]
RankingsWhere CHST3 stands among ~20K protein-coding genes
  • #9,428of 20,598
    Most Researched45
  • #1,219of 5,498
    Most Pathogenic Variants57 Β· top quartile
  • #11,524of 17,882
    Most Constrained (LOEUF)1.12
Genes detectedCHST3
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
CHST3, PGBD5, and SLIT2 can be identified as potential genes for the diagnosis and treatment of osteoporosis and sarcopenia.
PMID: 39747879
Sci Rep Β· 2025
1.00
2
A Chinese case of CHST3-related skeletal dysplasia and a systematic review.
PMID: 36729370
Endocrine Β· 2023
0.90
3
Recurrent c.776T>C mutation in CHST3 with four other novel mutations and a literature review.
PMID: 32639237
Clin Dysmorphol Β· 2020
0.80
4
Indian patients with CHST3-related chondrodysplasia with congenital joint dislocations.
PMID: 37876363
Am J Med Genet A Β· 2024
0.70
5
CHST3-related skeletal dysplasia in 14 patients: Identification of 8 novel variants and further expansion of the phenotypic spectrum.
PMID: 37183573
Am J Med Genet A Β· 2023
0.60