CDK5RAP3
CDK5 regulatory subunit associated protein 3
Basic information
Region (hg38): 17:47967810-47981781
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (69 variants)
- not_provided (1 variants)
- Pulmonary_hypoplasia (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDK5RAP3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000176096.3. 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 | 68 | 69 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 68 | 2 | 0 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CDK5RAP3 | protein_coding | protein_coding | ENST00000338399 | 14 | 13965 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 7.63e-15 | 0.217 | 124720 | 0 | 93 | 124813 | 0.000373 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.484 | 258 | 281 | 0.919 | 0.0000155 | 3262 |
| Missense in Polyphen | 79 | 92.162 | 0.85718 | 1169 | ||
| Synonymous | -0.453 | 124 | 118 | 1.05 | 0.00000686 | 989 |
| Loss of Function | 1.18 | 26 | 33.4 | 0.779 | 0.00000178 | 353 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000449 | 0.000449 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000556 | 0.0000556 |
| Finnish | 0.0000464 | 0.0000464 |
| European (Non-Finnish) | 0.000514 | 0.000512 |
| Middle Eastern | 0.0000556 | 0.0000556 |
| South Asian | 0.000524 | 0.000523 |
| Other | 0.000826 | 0.000824 |
dbNSFP
Source:
- Function
- FUNCTION: Probable tumor suppressor initially identified as a CDK5R1 interactor controlling cell proliferation (PubMed:12054757, PubMed:12737517). Negatively regulates NF-kappa-B-mediated gene transcription through the control of RELA phosphorylation (PubMed:17785205, PubMed:20228063). Also regulates mitotic G2/M transition checkpoint and mitotic G2 DNA damage checkpoint (PubMed:15790566, PubMed:19223857). Through its interaction with CDKN2A/ARF and MDM2 may induce MDM2-dependent p53/TP53 ubiquitination, stabilization and activation in the nucleus, thereby promoting G1 cell cycle arrest and inhibition of cell proliferation (PubMed:16173922). May play a role in the unfolded protein response, mediating the ufmylation of multiple proteins in response to endoplasmic reticulum stress (PubMed:23152784). May also play a role in the rupture of the nuclear envelope during apoptosis (PubMed:23478299). May regulate MAPK14 activity by regulating its dephosphorylation by PPM1D/WIP1 (PubMed:21283629). {ECO:0000269|PubMed:12054757, ECO:0000269|PubMed:12737517, ECO:0000269|PubMed:15790566, ECO:0000269|PubMed:16173922, ECO:0000269|PubMed:17785205, ECO:0000269|PubMed:19223857, ECO:0000269|PubMed:20228063, ECO:0000269|PubMed:21283629, ECO:0000269|PubMed:23152784, ECO:0000269|PubMed:23478299}.;
- 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
- 0.123
Intolerance Scores
- loftool
- 0.821
- rvis_EVS
- 0.62
- rvis_percentile_EVS
- 83.47
Haploinsufficiency Scores
- pHI
- 0.227
- hipred
- Y
- hipred_score
- 0.575
- ghis
- 0.478
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.941
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cdk5rap3
- 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);
Zebrafish Information Network
- Gene name
- cdk5rap3
- Affected structure
- blastoderm cell
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- regulation of cyclin-dependent protein serine/threonine kinase activity;negative regulation of protein phosphorylation;mitotic G2 DNA damage checkpoint;regulation of mitotic cell cycle;brain development;cell population proliferation;regulation of phosphatase activity;apoptotic nuclear changes;endoplasmic reticulum unfolded protein response;positive regulation of protein ubiquitination;negative regulation of NF-kappaB transcription factor activity;negative regulation of MAP kinase activity;negative regulation of protein kinase activity by regulation of protein phosphorylation;mitotic G2/M transition checkpoint;regulation of neuron differentiation;positive regulation of transcription by RNA polymerase II;protein ufmylation;negative regulation of protein serine/threonine kinase activity;positive regulation of protein localization to nucleus;positive regulation of signal transduction by p53 class mediator;negative regulation of cellular protein catabolic process;positive regulation of ubiquitin-dependent protein catabolic process
- Cellular component
- nucleus;nucleolus;cytoplasm;centrosome;cytosol;microtubule;membrane;protein-containing complex
- Molecular function
- protein binding;protein kinase binding;cyclin binding;ubiquitin-like protein ligase binding;mitogen-activated protein kinase binding;NF-kappaB binding;MDM2/MDM4 family protein binding