CHST5
protein-codingcarbohydrate sulfotransferase 5, the group of Sulfotransferases, membrane bound
Gene summary
The protein encoded by this gene belongs to the Gal/GalNAc/GlcNAc 6-O-sulfotransferase (GST) family, members of which catalyze the transfer of sulfate to position 6 of galactose (Gal), N-acetylgalactosamine (GalNAc), or N-acetylglucosamine (GlcNAc) residues within proteoglycans, and sulfation of O-linked sugars of mucin-type acceptors. Carbohydrate sulfation plays a critical role in many biologic processes. This gene is predominantly expressed in colon and small intestine. [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 ~7.6 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 CHST5 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_024533.5. 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 | 2 | |||
| missense | 67 | 8 | 3 | 78 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 69 | 9 | 3 | 81 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_078809.2 | 1 | MANE Select | |
| Ensembl | ENSP00000338783.3 | 1 | MANE Select | |
| Ensembl | ENSP00000454375.1 | 2 | Standard | |
| Ensembl | ENSP00000807753.1 | 1 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Metapathway biotransformation Phase I and II
- Metabolism of carbohydrates
- Keratan sulfate biosynthesis
- Keratan sulfate/keratin metabolism
- Glycosaminoglycan metabolism
Biological Process
- carbohydrate metabolic process
- N-acetylglucosamine metabolic process
- protein sulfation
- sulfur compound metabolic process
- keratan sulfate biosynthetic process
Molecular Function
- N-acetylglucosamine 6-O-sulfotransferase activity
- sulfotransferase activity
Cellular Component
- Golgi membrane
- Golgi apparatus
- trans-Golgi network
- integral component of membrane
- intrinsic component of Golgi membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000336257
- Coding exons
- 1
- Length
- 6713
- Individuals with no LoFs
- 125639
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 66
- Defined
- 125705
- p
- 0.000263
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.351 | 286 | 303 | 0.943 | 0.0000250 | 2583 |
| Missense (PolyPhen) | 130 | 147.46 | 0.88158 | 1275 | ||
| Synonymous | 0.107 | 146 | 148 | 0.989 | 0.0000132 | 933 |
| Loss of Function | 1.04 | 7 | 10.7 | 0.657 | 7.24e-7 | 82 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00044 | 0.00043 | rare |
| Latino/Admixed American | 0.00026 | 0.00026 | rare |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.00037 | 0.00037 | rare |
| South Asian | 0.000098 | 0.000098 | rare |
| Other | 0.00016 | 0.00016 | rare |
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 non-reducing N-acetylglucosamine (GlcNAc) residues and O-linked sugars of mucin-type acceptors. Acts on the non-reducing terminal GlcNAc of short carbohydrate substrates. However, it does not transfer sulfate to longer carbohydrate substrates that have poly-N-acetyllactosamine structures. Has no activity toward keratan. Not involved in generating HEV-expressed ligands for SELL. Its substrate specificity may be influenced by its subcellular location. {ECO:0000269|PubMed:10491328, ECO:0000269|PubMed:11352640, ECO:0000269|PubMed:12218059, ECO:0000269|PubMed:12626414}.;
Recessive Scores
- pRec
- 0.118
Intolerance Scores
- LoFtool
- 0.298
- RVIS EVS
- 0.22
- RVIS percentile EVS
- 68.38
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.235
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |