CHPF2
protein-codingchondroitin polymerizing factor 2, the group of Beta 3-glycosyltransferases|MicroRNA protein coding host genes|Beta 4-glycosyltransferases
Gene summary
Enables N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity. Involved in chondroitin sulfate proteoglycan biosynthetic process. Located in membrane. Is active in Golgi apparatus. [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 ~8.5 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 CHPF2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_019015.3. 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 | 3 | 4 | |||
| missense | 143 | 5 | 1 | 149 | ||
| nonsense | 2 | 2 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 146 | 8 | 1 | 155 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_061888.1 | 4 | MANE Select | |
| Ensembl | ENSP00000035307.2 | 4 | MANE Select | |
| RefSeq | NP_001271224.1 | 5 | Standard | |
| RefSeq | NP_001376580.1 | 3 | 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
- acetylgalactosaminyltransferase activity
- N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity
Cellular Component
- Golgi membrane
- membrane
- integral component of membrane
- Golgi cisterna membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000035307
- Coding exons
- 4
- Length
- 6334
- Individuals with no LoFs
- 125449
- Homozygous LoFs
- 2
- Heterozygous LoFs
- 296
- Defined
- 125747
- p
- 0.00119
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.516 | 518 | 486 | 1.07 | 0.0000337 | 4848 |
| Missense (PolyPhen) | 148 | 142.71 | 1.0371 | 1423 | ||
| Synonymous | 0.0855 | 200 | 202 | 0.992 | 0.0000118 | 1766 |
| Loss of Function | 0.656 | 28 | 32.0 | 0.875 | 0.00000248 | 260 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00088 | 0.00086 | rare |
| Latino/Admixed American | 0.00084 | 0.00084 | rare |
| Ashkenazi Jewish | 0.00020 | 0.00020 | rare |
| East Asian | 0.0029 | 0.0028 | notable |
| Finnish | 0.00042 | 0.00042 | rare |
| European (Non-Finnish) | 0.0011 | 0.0011 | notable |
| South Asian | 0.0022 | 0.0021 | notable |
| Other | 0.0012 | 0.0011 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Transfers glucuronic acid (GlcUA) from UDP-GlcUA to N- acetylgalactosamine residues on the non-reducing end of the elongating chondroitin polymer. Has no N- acetylgalactosaminyltransferase activity. {ECO:0000269|PubMed:12145278, ECO:0000269|PubMed:18316376}.;
Intolerance Scores
- LoFtool
- 0.962
- RVIS EVS
- 0.17
- RVIS percentile EVS
- 64.99
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.231
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |