CHST1
protein-codingcarbohydrate sulfotransferase 1, the group of Sulfotransferases, membrane bound
Gene summary
This locus encodes a member of the keratin sulfotransferase family of proteins. The encoded enzyme catalyzes the sulfation of the proteoglycan keratin. [provided by RefSeq, Aug 2011]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~17.9 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CHST1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_003654.6. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 36 | 1 | 37 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 37 | 1 | 0 | 38 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_003645.1 | 1 | MANE Select | |
| Ensembl | ENSP00000309270.2 | 1 | MANE Select | |
| Ensembl | ENSP00000561855.1 | 1 | Standard | |
| Ensembl | ENSP00000561855.1 | 1 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Glycosaminoglycan biosynthesis - keratan sulfate - Homo sapiens (human)
- Metapathway biotransformation Phase I and II
- Metabolism of carbohydrates
- Keratan sulfate biosynthesis
- Keratan sulfate/keratin metabolism
Biological Process
- polysaccharide metabolic process
- galactose metabolic process
- N-acetylglucosamine metabolic process
- sulfur compound metabolic process
- inflammatory response
Molecular Function
- N-acetylglucosamine 6-O-sulfotransferase activity
- sulfotransferase activity
- keratan sulfotransferase activity
Cellular Component
- Golgi membrane
- trans-Golgi network
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000308064
- Coding exons
- 1
- Length
- 16746
- Individuals with no LoFs
- 125734
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 10
- Defined
- 125744
- p
- 0.0000398
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.95 | 161 | 306 | 0.525 | 0.0000238 | 2613 |
| Missense (PolyPhen) | 57 | 140.15 | 0.40672 | 1218 | ||
| Synonymous | 2.12 | 118 | 151 | 0.781 | 0.0000128 | 898 |
| Loss of Function | 2.91 | 2 | 13.6 | 0.147 | 8.45e-7 | 113 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000062 | 0.000062 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Sulfotransferase that utilizes 3'-phospho-5'-adenylyl sulfate (PAPS) as sulfonate donor to catalyze the transfer of sulfate to position 6 of galactose (Gal) residues of keratan. Has a preference for sulfating keratan sulfate, but it also transfers sulfate to the unsulfated polymer. The sulfotransferase activity on sialyl LacNAc structures is much higher than the corresponding desialylated substrate, and only internal Gal residues are sulfated. May function in the sulfation of sialyl N- acetyllactosamine oligosaccharide chains attached to glycoproteins. Participates in biosynthesis of selectin ligands. Selectin ligands are present in high endothelial cells (HEVs) and play a central role in lymphocyte homing at sites of inflammation. {ECO:0000269|PubMed:10330415, ECO:0000269|PubMed:10642612}.;
Recessive Scores
- pRec
- 0.149
Intolerance Scores
- LoFtool
- 0.0319
- RVIS EVS
- -0.25
- RVIS percentile EVS
- 35.75
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.746
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |