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Gene
CHST3
carbohydrate sulfotransferase 3
- HGNC 1971↗(opens in a new tab)
- Ensembl gene ENSG00000122863↗(opens in a new tab)
- NCBI Gene 9469↗(opens in a new tab)
Summary
- Cytogenetic location
- 10q22.1
- Coordinates
- Chromosome 10: 71,964,395–72,013,558 (GRCh38)
- Exons
- 3 exons across 49.2 kb
- Protein
- 479 amino acids
- Also known as
- C6ST, C6ST1
- MANE Select transcript
- ENST00000373115.5NM_004273.5
- Locus type
- Protein-coding
- Very high
- Confident
- Low
- Very low
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This page as data
Add .json to the page's address, or ask for application/json, to read it as JSON.
library(jsonlite)
url <- "https://dantelabs.com/genes/chst3.json"
page <- fromJSON(url)
page$gene$nameCHST310q22.1
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No Genome Test report reads CHST3 yet. The test sequences your whole genome, so your data includes it all the same.
How CHST3 is laid out
- Coding sequence
- Untranslated region
- Intron
- Direction of transcription
- Known disease-causing sites
- Stretches short reads find hard
Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.
Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).
Nearby genes from Ensembl release 116, on GRCh38.
Exons make up 6.9 kb of the gene's 49.2 kb; 1,440 of those bases code for the protein.
Sequencing CHST3
3Easy
How hard CHST3 is to sequence with short reads, out of 100
0 · Easy100 · Hard
Almost all of CHST3's exons sit where short reads map cleanly.
What adds to it: the share of CHST3's exons in each kind of hard region
- MappabilityStretches where 100 or 250 bp reads cannot be placed uniquely, so a call there may be missing or wrong. Weight 35%.0%
- HomologySegmental duplications: copies elsewhere in the genome, such as paralogues and pseudogenes, at 90% identity or more. Weight 30%.0%
- RepeatsTandem repeats and runs of one base, which reads slip on and may not span. Weight 15%.2.6%
- GC contentWindows under 25% or over 65% G and C, which library preparation covers thinly. Weight 10%.23%
- Reference coverageGaps in the reference assembly nearby, where there is no sequence for reads to align to. Weight 10%.0%
A Dante Labs score from our own research, built on NIST's Genome in a Bottle maps of hard-to-sequence regions.How it's scoredEach bar is the share of CHST3's exon bases in that kind of difficult region. The score weighs them by how much each costs a short-read call: 0 when no base is in any, 100 when every base is in all of them.
44
positions in CHST3 where ClinVar classes a change as pathogenic or likely pathogenic
None of them falls in a region short reads find hard.
A whole genome covers all 49.2 kb of CHST3, introns included, not only the 6.9 kb of exons.
ClinVar pathogenic variants (45)
The CHST3 variants ClinVar classifies pathogenic or likely pathogenic for any condition, reviewed by at least one submitter with criteria, and the most reviewed of them. It is ClinVar's public record of the gene, never a result.
- Pathogenic 24
- Pathogenic/likely pathogenic 2
- Likely pathogenic 19
| Variant | Conditions | ClinVar classification | Review status |
|---|---|---|---|
| NM_004273.5(CHST3):c.533dup (p.Ala179fs) (opens in a new tab) | spondyloepiphyseal dysplasia with congenital joint dislocations | Pathogenic/likely pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_004273.5(CHST3):c.661C>T (p.Arg221Cys) (opens in a new tab) | spondyloepiphyseal dysplasia with congenital joint dislocations | Pathogenic/likely pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_004273.5(CHST3):c.58_77dup (p.Leu26_Phe27insTer) (opens in a new tab) | spondyloepiphyseal dysplasia with congenital joint dislocations | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_004273.5(CHST3):c.83T>A (p.Leu28Ter) (opens in a new tab) | spondyloepiphyseal dysplasia with congenital joint dislocations | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_004273.5(CHST3):c.141-1G>C (opens in a new tab) | spondyloepiphyseal dysplasia with congenital joint dislocations | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_004273.5(CHST3):c.238del (p.Ser79_Leu80insTer) (opens in a new tab) | spondyloepiphyseal dysplasia with congenital joint dislocations | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_004273.5(CHST3):c.271C>T (p.Gln91Ter) (opens in a new tab) | spondyloepiphyseal dysplasia with congenital joint dislocations | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_004273.5(CHST3):c.334G>T (p.Glu112Ter) (opens in a new tab) | spondyloepiphyseal dysplasia with congenital joint dislocations | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_004273.5(CHST3):c.362dup (p.Glu122fs) (opens in a new tab) | spondyloepiphyseal dysplasia with congenital joint dislocations | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_004273.5(CHST3):c.375_378dup (p.Ala127fs) (opens in a new tab) | spondyloepiphyseal dysplasia with congenital joint dislocations | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_004273.5(CHST3):c.475T>A (p.Phe159Ile) (opens in a new tab) | spondyloepiphyseal dysplasia with congenital joint dislocations | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_004273.5(CHST3):c.491C>T (p.Pro164Leu) (opens in a new tab) | spondyloepiphyseal dysplasia with congenital joint dislocations | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_004273.5(CHST3):c.512_513del (p.Thr171fs) (opens in a new tab) | spondyloepiphyseal dysplasia with congenital joint dislocations | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_004273.5(CHST3):c.685_686del (p.Cys229fs) (opens in a new tab) | spondyloepiphyseal dysplasia with congenital joint dislocations | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_004273.5(CHST3):c.688G>T (p.Glu230Ter) (opens in a new tab) | spondyloepiphyseal dysplasia with congenital joint dislocations | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_004273.5(CHST3):c.696dup (p.Val233fs) (opens in a new tab) | spondyloepiphyseal dysplasia with congenital joint dislocations | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_004273.5(CHST3):c.718A>T (p.Lys240Ter) (opens in a new tab) | spondyloepiphyseal dysplasia with congenital joint dislocations | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_004273.5(CHST3):c.723dup (p.Phe242fs) (opens in a new tab) | spondyloepiphyseal dysplasia with congenital joint dislocations | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_004273.5(CHST3):c.763del (p.Leu255fs) (opens in a new tab) | spondyloepiphyseal dysplasia with congenital joint dislocations | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_004273.5(CHST3):c.802G>T (p.Glu268Ter) (opens in a new tab) | spondyloepiphyseal dysplasia with congenital joint dislocations | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_004273.5(CHST3):c.855del (p.Leu286fs) (opens in a new tab) | spondyloepiphyseal dysplasia with congenital joint dislocations | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_004273.5(CHST3):c.904G>C (p.Asp302His) (opens in a new tab) | spondyloepiphyseal dysplasia with congenital joint dislocations | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_004273.5(CHST3):c.976dup (p.Asp326fs) (opens in a new tab) | spondyloepiphyseal dysplasia with congenital joint dislocations | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_004273.5(CHST3):c.1150_1166del (p.Glu384fs) (opens in a new tab) | spondyloepiphyseal dysplasia with congenital joint dislocations | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_004273.5(CHST3):c.1177del (p.Pro392_Leu393insTer) (opens in a new tab) | spondyloepiphyseal dysplasia with congenital joint dislocations | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
See all 45 with every other CHST3 variant in ClinVar → (opens in a new tab)
Traits linked to CHST3
The Human Phenotype Ontology lists these as features of the rare conditions CHST3 can cause. Each trait's page lists the other genes linked to it.
Abnormality of the musculoskeletal system
- Intervertebral space narrowing
- Limited hip extension
- Scoliosis
- Small end part of bone
- Abnormal vertebral body morphology
- Barrel-shaped chest
- Disproportionate short-trunked short stature
- Enlarged joints
Show 31 more traits
- Flexed joint that cannot be straightened
- Generalized decreased muscle tone
- Irregular end part of long bone
- Multiple joint dislocation
- Osteopenia
- Double-Jointed
- Kyphoscoliosis
- Recurrent fractures
- 11 pairs of ribs
- Congenital diaphragmatic hernia
- Delayed bone maturation
- Flattened vertebrae
- Generalized osteoporosis
- Pigeon chest
- Shoulder dislocation
- Advanced bone age
- Coronal cleft vertebrae
- Decreased hip abduction
- Disease of the joints
- Excessive inward curvature of lower spine
- Flat end part of bone
- Generalized bone demineralization
- Hunched back
- Irregular vertebral endplates
- Joint dislocation
- Low muscle tone
- Narrow chest
- Narrow vertebral interpedicular distance
- Osteoporosis
- Shield chest
- Spondyloepiphyseal dysplasia
Abnormality of limbs
- Club feet
- Dislocated radial head
- Fused forearm bones
- Knee dislocation
- Abnormality of the elbow
- Disproportionately short upper portion of limb
- Knock knees
- Outward turned elbows
Show 29 more traits
- Short fingers or toes
- Back knee
- Bunion
- Dropped arches
- Flared wide portion of long bone
- Gap between 1st and 2nd toes
- Shortened long bone of hand
- Metacarpophalangeal joint hyperextensibility
- Bilateral single transverse palmar creases
- Bowed shankbone
- Broad outermost hand bones
- Curving of inner forearm bone
- Dislocated elbows on both sides
- Displaced little finger
- Elbow dislocation
- Elbow flexion contracture
- Enlarged wide portion of a long bone
- Fixed elbow flexion
- Front half of foot turns inward
- Hip dislocation
- Multiple carpal ossification centers
- Permanent flexion of the finger
- Short finger bones
- Short neck of thighbone
- Short outermost finger bone
- Small innermost thighbone end part
- Spoon shaped thumbs
- Talipes equinovalgus
- Underdeveloped inner large forearm bone
Abnormality of the cardiovascular system
- Abnormal cardiovascular system morphology
- An opening in the wall separating the top two chambers of the heart
- Aortic regurgitation
- Aortic valve has two leaflets rather than three
- Bulge in wall of root of large artery that carries blood away from heart
- Enlarged heart
- Hole in heart wall separating two lower heart chambers
- Increased blood pressure in blood vessels of lungs
External links
Gene records
Transcript
Protein
Where this comes from
- HGNC: the gene's symbol, name, other symbols and location.
- MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
- ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
- The Genome in a Bottle genome stratifications, from NIST: the sequencing difficulty score.
- The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
- Data release 2026.10.17-8666dff2.
Cite this page
Dante Labs. (n.d.). CHST3 gene: carbohydrate sulfotransferase 3. Retrieved 18 October 2026, from https://dantelabs.com/genes/chst3
Dante Labs. CHST3 gene: carbohydrate sulfotransferase 3 [Internet]. [cited 18 October 2026]. Available from: https://dantelabs.com/genes/chst3
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