CDK7
cyclin dependent kinase 7, the group of Cyclin dependent kinases|CDK activating kinase complex
Basic information
Region (hg38): 5:69234794-69277430
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDK7 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 | 0 | |||||
| missense | 8 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 7 | 1 | 0 |
Variants in CDK7
This is a list of pathogenic ClinVar variants found in the CDK7 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 5-69234982-C-G | not specified | Likely benign (Jun 24, 2022) | ||
| 5-69235407-A-G | not specified | Uncertain significance (Jan 10, 2023) | ||
| 5-69235430-A-T | not specified | Uncertain significance (Apr 06, 2023) | ||
| 5-69259894-T-C | not specified | Uncertain significance (May 24, 2023) | ||
| 5-69262264-T-C | not specified | Uncertain significance (May 06, 2024) | ||
| 5-69272976-G-A | not specified | Uncertain significance (Nov 23, 2022) | ||
| 5-69276550-A-T | not specified | Uncertain significance (Nov 13, 2023) | ||
| 5-69276605-A-T | not specified | Uncertain significance (Jan 27, 2022) | ||
| 5-69276648-G-C | not specified | Uncertain significance (Oct 25, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CDK7 | protein_coding | protein_coding | ENST00000256443 | 12 | 42583 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 4.47e-7 | 0.843 | 125715 | 0 | 31 | 125746 | 0.000123 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.94 | 106 | 179 | 0.592 | 0.00000826 | 2246 |
| Missense in Polyphen | 45 | 82.883 | 0.54294 | 1001 | ||
| Synonymous | 0.467 | 58 | 62.7 | 0.925 | 0.00000307 | 643 |
| Loss of Function | 1.49 | 13 | 20.2 | 0.642 | 9.18e-7 | 267 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000155 | 0.000155 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000452 | 0.000435 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.000125 | 0.000123 |
| Middle Eastern | 0.000452 | 0.000435 |
| South Asian | 0.0000337 | 0.0000327 |
| Other | 0.000340 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Serine/threonine kinase involved in cell cycle control and in RNA polymerase II-mediated RNA transcription. Cyclin- dependent kinases (CDKs) are activated by the binding to a cyclin and mediate the progression through the cell cycle. Each different complex controls a specific transition between 2 subsequent phases in the cell cycle. Required for both activation and complex formation of CDK1/cyclin-B during G2-M transition, and for activation of CDK2/cyclins during G1-S transition (but not complex formation). CDK7 is the catalytic subunit of the CDK-activating kinase (CAK) complex. Phosphorylates SPT5/SUPT5H, SF1/NR5A1, POLR2A, p53/TP53, CDK1, CDK2, CDK4, CDK6 and CDK11B/CDK11. CAK activates the cyclin-associated kinases CDK1, CDK2, CDK4 and CDK6 by threonine phosphorylation, thus regulating cell cycle progression. CAK complexed to the core-TFIIH basal transcription factor activates RNA polymerase II by serine phosphorylation of the repetitive C-terminal domain (CTD) of its large subunit (POLR2A), allowing its escape from the promoter and elongation of the transcripts. Phosphorylation of POLR2A in complex with DNA promotes transcription initiation by triggering dissociation from DNA. Its expression and activity are constant throughout the cell cycle. Upon DNA damage, triggers p53/TP53 activation by phosphorylation, but is inactivated in turn by p53/TP53; this feedback loop may lead to an arrest of the cell cycle and of the transcription, helping in cell recovery, or to apoptosis. Required for DNA-bound peptides-mediated transcription and cellular growth inhibition. {ECO:0000269|PubMed:10024882, ECO:0000269|PubMed:11113184, ECO:0000269|PubMed:16327805, ECO:0000269|PubMed:17373709, ECO:0000269|PubMed:17386261, ECO:0000269|PubMed:17901130, ECO:0000269|PubMed:19015234, ECO:0000269|PubMed:19071173, ECO:0000269|PubMed:19136461, ECO:0000269|PubMed:19450536, ECO:0000269|PubMed:19667075, ECO:0000269|PubMed:20360007, ECO:0000269|PubMed:9372954, ECO:0000269|PubMed:9840937}.;
- Pathway
- Nucleotide excision repair - Homo sapiens (human);Cell cycle - Homo sapiens (human);Basal transcription factors - Homo sapiens (human);MicroRNAs in cardiomyocyte hypertrophy;Integrated Breast Cancer Pathway;Cardiac Hypertrophic Response;Eukaryotic Transcription Initiation;G1 to S cell cycle control;DNA Repair;Disease;RNA Pol II CTD phosphorylation and interaction with CE during HIV infection;NoRC negatively regulates rRNA expression;Negative epigenetic regulation of rRNA expression;Formation of the HIV-1 Early Elongation Complex;Epigenetic regulation of gene expression;Gene expression (Transcription);sonic hedgehog receptor ptc1 regulates cell cycle;Formation of HIV-1 elongation complex containing HIV-1 Tat;Tat-mediated elongation of the HIV-1 transcript;HIV Transcription Elongation;estrogen responsive protein efp controls cell cycle and breast tumors growth;cyclins and cell cycle regulation;Formation of HIV elongation complex in the absence of HIV Tat;Generic Transcription Pathway;Transcription of the HIV genome;Late Phase of HIV Life Cycle;HIV Life Cycle;HIV Infection;RNA Polymerase II HIV Promoter Escape;RNA Polymerase II Pre-transcription Events;RNA Polymerase II Transcription Initiation;RNA Polymerase II Transcription Initiation And Promoter Clearance;RNA Pol II CTD phosphorylation and interaction with CE;Formation of RNA Pol II elongation complex ;RNA Polymerase I Promoter Clearance;HIV Transcription Initiation;RNA polymerase II transcribes snRNA genes;RNA Polymerase II Transcription;Metabolism of RNA;Infectious disease;RNA Polymerase I Transcription Termination;RNA Polymerase I Transcription;Cyclin D associated events in G1;G1 Phase;RNA Polymerase II Transcription Elongation;Cyclin E associated events during G1/S transition ;RNA Polymerase I Transcription Initiation;RNA Polymerase I Promoter Escape;Mitotic G1-G1/S phases;Cyclin A:Cdk2-associated events at S phase entry;BCR;RNA Polymerase II Promoter Escape;RNA Polymerase I Chain Elongation;AndrogenReceptor;S Phase;RNA Polymerase II Transcription Pre-Initiation And Promoter Opening;Cyclin A/B1/B2 associated events during G2/M transition;IL-7 signaling;TP53 Regulates Transcription of DNA Repair Genes;G2/M Transition;Mitotic G2-G2/M phases;JAK STAT pathway and regulation;G1/S Transition;EPO signaling;Transcriptional Regulation by TP53;mRNA Capping;Formation of the Early Elongation Complex;RUNX1 regulates transcription of genes involved in differentiation of HSCs;Cell Cycle;Formation of Incision Complex in GG-NER;VEGF;Global Genome Nucleotide Excision Repair (GG-NER);Cell Cycle, Mitotic;Formation of TC-NER Pre-Incision Complex;Transcriptional regulation by RUNX1;Retinoic acid receptors-mediated signaling;Dual incision in TC-NER;Gap-filling DNA repair synthesis and ligation in TC-NER;Transcription-Coupled Nucleotide Excision Repair (TC-NER);Nucleotide Excision Repair
(Consensus)
Recessive Scores
- pRec
- 0.488
Intolerance Scores
- loftool
- 0.724
- rvis_EVS
- 0.06
- rvis_percentile_EVS
- 58.26
Haploinsufficiency Scores
- pHI
- 0.696
- hipred
- Y
- hipred_score
- 0.672
- ghis
- 0.546
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.981
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cdk7
- Phenotype
- embryo phenotype; pigmentation phenotype; hematopoietic system 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); digestive/alimentary phenotype; skeleton phenotype; renal/urinary system phenotype; cellular phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan);
Gene ontology
- Biological process
- regulation of cyclin-dependent protein serine/threonine kinase activity;transcription-coupled nucleotide-excision repair;nucleotide-excision repair, preincision complex assembly;transcription initiation from RNA polymerase I promoter;termination of RNA polymerase I transcription;transcription by RNA polymerase II;transcription initiation from RNA polymerase II promoter;transcription elongation from RNA polymerase II promoter;7-methylguanosine mRNA capping;protein phosphorylation;cell cycle arrest;cell population proliferation;androgen receptor signaling pathway;snRNA transcription by RNA polymerase II;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;protein stabilization;cell division
- Cellular component
- nucleus;nucleoplasm;transcription factor TFIIH holo complex;cytoplasm;cyclin-dependent protein kinase activating kinase holoenzyme complex;perinuclear region of cytoplasm;transcription factor TFIIK complex
- Molecular function
- transcription coactivator activity;protein kinase activity;protein serine/threonine kinase activity;cyclin-dependent protein serine/threonine kinase activity;protein binding;ATP binding;protein C-terminus binding;DNA-dependent ATPase activity;RNA polymerase II CTD heptapeptide repeat kinase activity;kinase activity;androgen receptor binding