CPLANE2
protein-codingciliogenesis and planar polarity effector complex subunit 2, the group of Ciliogenesis and planar polarity effector complex subunits
Gene summary
Predicted to enable GTP binding activity and GTPase activity. Predicted to be involved in axoneme assembly; intracellular protein localization; and regulation of vesicle-mediated transport. Predicted to act upstream of or within several processes, including endocardial cushion fusion; regulation of smoothened signaling pathway; and smoothened signaling pathway. Located in centriole; ciliary basal body; and ciliary transition zone. [provided by Alliance of Genome Resources, Jun 2026]
- C1orf89
- RSG1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~5.5 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 CPLANE2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_030907.4. 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 | 1 | 1 | 2 | |||
| missense | 55 | 3 | 58 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 58 | 4 | 0 | 62 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_112169.2 | 5 | MANE Select | |
| Ensembl | ENSP00000364749.2 | 5 | MANE Select | |
| Ensembl | ENSP00000406390.1 | 4 | Standard | |
| Ensembl | ENSP00000615500.1 | 5 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- exocytosis
- protein transport
- regulation of exocytosis
- regulation of vesicle fusion
- cellular protein localization
Molecular Function
- GTPase activity
- protein binding
- GTP binding
Cellular Component
- nucleoplasm
- cytoplasm
- ciliary basal body
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000375599
- Coding exons
- 5
- Length
- 5463
- Individuals with no LoFs
- 125722
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 23
- Defined
- 125745
- p
- 0.0000915
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.617 | 152 | 175 | 0.869 | 0.0000112 | 1650 |
| Missense (PolyPhen) | 47 | 49.786 | 0.94404 | 492 | ||
| Synonymous | 1.61 | 53 | 70.1 | 0.756 | 0.00000432 | 555 |
| Loss of Function | 0.205 | 8 | 8.65 | 0.925 | 3.68e-7 | 98 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00026 | 0.00025 | rare |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.00028 | 0.00028 | rare |
| European (Non-Finnish) | 0.000081 | 0.000079 | rare |
| South Asian | 0.000098 | 0.000098 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Potential effector of the planar cell polarity signaling pathway. Plays a role in targeted membrane trafficking most probably at the level of vesicle fusion with membranes. Involved in cilium biogenesis by regulating the transport of cargo proteins to the basal body and to the apical tips of cilia. More generally involved in exocytosis in secretory cells (By similarity). {ECO:0000250|UniProtKB:Q6GNL4}.;
Recessive Scores
- pRec
- 0.102
Intolerance Scores
- RVIS EVS
- -0.12
- RVIS percentile EVS
- 45.13
Essentials
- Essential (gene trap)
- N