CSPG5
protein-codingchondroitin sulfate proteoglycan 5
Gene summary
The protein encoded by this gene is a proteoglycan that may function as a neural growth and differentiation factor. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2011]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~18.6 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 CSPG5 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_006574.4. 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 | 3 | 1 | 4 | |||
| missense | 77 | 77 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 77 | 3 | 1 | 81 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_006565.2 | 5 | MANE Select | |
| Ensembl | ENSP00000264723.4 | 5 | MANE Select | |
| RefSeq | NP_001193871.1 | 4 | Standard | |
| RefSeq | NP_001193872.1 | 5 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Metabolism of carbohydrates
- A tetrasaccharide linker sequence is required for GAG synthesis
- Heparan sulfate/heparin (HS-GAG) metabolism
- Chondroitin sulfate biosynthesis
- Dermatan sulfate biosynthesis
Biological Process
- nervous system development
- regulation of signaling receptor activity
- cell differentiation
- chondroitin sulfate biosynthetic process
- chondroitin sulfate catabolic process
Molecular Function
- protein binding
- growth factor activity
Cellular Component
- Golgi membrane
- extracellular region
- endoplasmic reticulum membrane
- Golgi apparatus
- Golgi lumen
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000383738
- Coding exons
- 5
- Length
- 18554
- Individuals with no LoFs
- 125741
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 7
- Defined
- 125748
- p
- 0.0000278
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.34 | 251 | 318 | 0.788 | 0.0000180 | 3637 |
| Missense (PolyPhen) | 87 | 139.05 | 0.62565 | 1546 | ||
| Synonymous | 1.04 | 124 | 140 | 0.888 | 0.00000883 | 1193 |
| Loss of Function | 2.56 | 5 | 16.1 | 0.311 | 6.84e-7 | 209 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0.000059 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000027 | 0.000026 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May function as a growth and differentiation factor involved in neuritogenesis. May induce ERBB3 activation. {ECO:0000269|PubMed:15358134}.;
Recessive Scores
- pRec
- 0.155
Intolerance Scores
- LoFtool
- 0.368
- RVIS EVS
- 0.02
- RVIS percentile EVS
- 55.45
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- H
- Indispensability pred.
- N
- Indispensability score
- 0.406
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |