CCNL2
protein-codingcyclin L2, the group of Cyclins
Gene summary
The protein encoded by this gene belongs to the cyclin family. Through its interaction with several proteins, such as RNA polymerase II, splicing factors, and cyclin-dependent kinases, this protein functions as a regulator of the pre-mRNA splicing process, as well as in inducing apoptosis by modulating the expression of apoptotic and antiapoptotic proteins. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Aug 2011]
- CCNM
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~13.6 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 CCNL2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_030937.6. 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 | 4 | 4 | ||||
| missense | 99 | 3 | 102 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 0 | 0 | 104 | 7 | 0 | 111 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_112199.2 | 11 | MANE Select | |
| Ensembl | ENSP00000383611.3 | 11 | MANE Select | |
| RefSeq | NP_001034666.1 | 6 | Standard | |
| RefSeq | NP_001307082.1 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- regulation of cyclin-dependent protein serine/threonine kinase activity
- regulation of transcription by RNA polymerase II
Molecular Function
- protein binding
- cyclin-dependent protein serine/threonine kinase regulator activity
Cellular Component
- nucleus
- nucleoplasm
- nuclear speck
- intracellular membrane-bounded organelle
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000400809
- Coding exons
- 11
- Length
- 13618
- Individuals with no LoFs
- 112711
- Homozygous LoFs
- 449
- Heterozygous LoFs
- 12588
- Defined
- 125748
- p
- 0.0533
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.538 | 312 | 340 | 0.918 | 0.0000222 | 3315 |
| Missense (PolyPhen) | 100 | 141.71 | 0.70568 | 1486 | ||
| Synonymous | -1.20 | 152 | 134 | 1.13 | 0.00000799 | 1084 |
| Loss of Function | 3.68 | 7 | 28.0 | 0.250 | 0.00000177 | 296 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.084 | 0.084 | notable |
| Latino/Admixed American | 0.023 | 0.023 | notable |
| Ashkenazi Jewish | 0.026 | 0.027 | notable |
| East Asian | 0.084 | 0.084 | notable |
| Finnish | 0.10 | 0.10 | notable |
| European (Non-Finnish) | 0.040 | 0.040 | notable |
| South Asian | 0.079 | 0.079 | notable |
| Other | 0.058 | 0.058 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Involved in pre-mRNA splicing. May induce cell death, possibly by acting on the transcription and RNA processing of apoptosis-related factors. {ECO:0000269|PubMed:14684736, ECO:0000269|PubMed:18216018}.;
Recessive Scores
- pRec
- 0.107
Intolerance Scores
- LoFtool
- 0.634
- RVIS EVS
- 0.0000761
- RVIS percentile EVS
- 53.98
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.962
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |