CDK2AP1
Basic information
Region (hg38): 12:123250111-123272334
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- Combined oxidative phosphorylation defect type 7;Spastic paraplegia (53 variants)
- not provided (42 variants)
- Combined oxidative phosphorylation defect type 7 (41 variants)
- Spastic paraplegia;Combined oxidative phosphorylation defect type 7 (29 variants)
- Hereditary spastic paraplegia (11 variants)
- not specified (8 variants)
- Hereditary spastic paraplegia 55 (6 variants)
- Combined oxidative phosphorylation deficiency (4 variants)
- Inborn genetic diseases (3 variants)
- Hereditary spastic paraplegia 55;Combined oxidative phosphorylation defect type 7 (1 variants)
- MTRFR-related condition (1 variants)
- Epileptic encephalopathy (1 variants)
- Abnormal brain morphology (1 variants)
- Neurodevelopmental disorder (1 variants)
- Combined oxidative phosphorylation defect type 7;Hereditary spastic paraplegia 55 (1 variants)
- Hereditary motor and sensory neuropathy with optic atrophy (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDK2AP1 gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | |||||
| missense | 3 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region ? | 1 | 1 | ||||
| non coding ? | 78 | 30 | 133 | |||
| Total | 8 | 9 | 81 | 30 | 10 |
Highest pathogenic variant AF is 0.000118
Variants in CDK2AP1
This is a list of pathogenic ClinVar variants found in the CDK2AP1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CDK2AP1 | protein_coding | protein_coding | ENST00000261692 | 4 | 11354 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.448 | 0.526 | 125742 | 0 | 2 | 125744 | 0.00000795 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.42 | 35 | 67.9 | 0.515 | 0.00000456 | 723 |
| Missense in Polyphen | 7 | 20.389 | 0.34333 | 244 | ||
| Synonymous | 0.168 | 27 | 28.1 | 0.960 | 0.00000210 | 226 |
| Loss of Function | 1.79 | 1 | 5.53 | 0.181 | 2.36e-7 | 69 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000176 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: specific inhibitor of the cell-cycle kinase CDK2. {ECO:0000250}.;
Recessive Scores
- pRec
- 0.156
Intolerance Scores
- loftool
- 0.180
- rvis_EVS
- -0.03
- rvis_percentile_EVS
- 51.04
Haploinsufficiency Scores
- pHI
- 0.697
- hipred
- Y
- hipred_score
- 0.688
- ghis
- 0.613
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.923
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cdk2ap1
- Phenotype
- craniofacial phenotype; cellular phenotype; growth/size/body region phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);
Gene ontology
- Biological process
- positive regulation of protein phosphorylation;DNA-dependent DNA replication;cell cycle
- Cellular component
- nucleus;nucleoplasm;cytosol;perinuclear region of cytoplasm
- Molecular function
- protein binding;DNA polymerase binding