CDK5RAP1
Basic information
Region (hg38): 20:33358839-33401561
Previous symbols: [ "C20orf34" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (63 variants)
- not_provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDK5RAP1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000016408.4. Only rare variants are included in the table.
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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 1 | |||||
missense | 60 | 62 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 60 | 3 | 0 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
CDK5RAP1 | protein_coding | protein_coding | ENST00000346416 | 13 | 42723 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
7.78e-19 | 0.00395 | 125615 | 0 | 133 | 125748 | 0.000529 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.25 | 277 | 342 | 0.810 | 0.0000192 | 3846 |
Missense in Polyphen | 94 | 134.45 | 0.69914 | 1509 | ||
Synonymous | 0.364 | 117 | 122 | 0.958 | 0.00000641 | 1154 |
Loss of Function | 0.0555 | 28 | 28.3 | 0.989 | 0.00000137 | 337 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000605 | 0.000605 |
Ashkenazi Jewish | 0.000101 | 0.0000992 |
East Asian | 0.000708 | 0.000707 |
Finnish | 0.0000924 | 0.0000924 |
European (Non-Finnish) | 0.000758 | 0.000756 |
Middle Eastern | 0.000708 | 0.000707 |
South Asian | 0.000557 | 0.000555 |
Other | 0.000167 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Specifically inhibits CDK5 activation by CDK5R1.;
- Pathway
- miR-targeted genes in epithelium - TarBase;miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase
(Consensus)
Recessive Scores
- pRec
- 0.124
Intolerance Scores
- loftool
- 0.271
- rvis_EVS
- -0.8
- rvis_percentile_EVS
- 12.46
Haploinsufficiency Scores
- pHI
- 0.101
- hipred
- N
- hipred_score
- 0.407
- ghis
- 0.574
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.974
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cdk5rap1
- Phenotype
- behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); muscle phenotype; homeostasis/metabolism phenotype; cellular phenotype;
Gene ontology
- Biological process
- brain development;tRNA methylthiolation;regulation of neuron differentiation;negative regulation of cyclin-dependent protein serine/threonine kinase activity;positive regulation of translational fidelity;positive regulation of mitochondrial translation;mitochondrial tRNA modification
- Cellular component
- cellular_component;mitochondrion
- Molecular function
- protein kinase binding;N6-isopentenyladenosine methylthiotransferase activity;protein-containing complex binding;metal ion binding;4 iron, 4 sulfur cluster binding