CHPF
protein-codingchondroitin polymerizing factor, the group of Beta 4-glycosyltransferases|Beta 3-glycosyltransferases
Gene summary
Enables N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity and glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity. Involved in chondroitin sulfate proteoglycan biosynthetic process. Located in cytosol. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~4.9 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 CHPF variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_024536.6. 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 | 2 | |||
| missense | 123 | 4 | 127 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 124 | 4 | 1 | 129 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_078812.3 | 4 | MANE Select | |
| Ensembl | ENSP00000243776.6 | 4 | MANE Select | |
| RefSeq | NP_001182660.2 | 3 | Standard | |
| Ensembl | ENSP00000362998.2 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate - Homo sapiens (human)
- Metabolism of carbohydrates
- Chondroitin sulfate biosynthesis
- Chondroitin sulfate/dermatan sulfate metabolism
- Glycosaminoglycan metabolism
Biological Process
- chondroitin sulfate biosynthetic process
Molecular Function
- metal ion binding
- glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity
- N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity
Cellular Component
- Golgi membrane
- mitochondrial matrix
- cytosol
- integral component of membrane
- Golgi cisterna membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000243776
- Coding exons
- 4
- Length
- 4841
- Individuals with no LoFs
- 125678
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 68
- Defined
- 125746
- p
- 0.000270
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.03 | 419 | 483 | 0.868 | 0.0000317 | 4803 |
| Missense (PolyPhen) | 87 | 113.4 | 0.7672 | 1155 | ||
| Synonymous | 1.18 | 188 | 210 | 0.896 | 0.0000125 | 1762 |
| Loss of Function | 3.33 | 6 | 23.4 | 0.257 | 0.00000143 | 218 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00019 | 0.00018 | rare |
| Latino/Admixed American | 0.00017 | 0.00017 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000055 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00051 | 0.00048 | rare |
| South Asian | 0.000069 | 0.000065 | rare |
| Other | 0.00017 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- 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. Isoform 2 may facilitate PRKN transport into the mitochondria. In collaboration with PRKN, isoform 2 may enhance cell viability and protect cells from oxidative stress. {ECO:0000269|PubMed:12761225}.;
Recessive Scores
- pRec
- 0.196
Intolerance Scores
- RVIS EVS
- -0.86
- RVIS percentile EVS
- 10.89
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.323
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |