CCNC
cyclin C, the group of Cyclins|Mediator complex
Basic information
Region (hg38): 6:99542387-99568825
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 CCNC 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 | 9 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 9 | 0 | 0 |
Variants in CCNC
This is a list of pathogenic ClinVar variants found in the CCNC region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 6-99545143-T-G | not specified | Uncertain significance (Jan 08, 2024) | ||
| 6-99545155-T-C | not specified | Uncertain significance (Jul 16, 2021) | ||
| 6-99546446-C-A | not specified | Uncertain significance (Feb 05, 2024) | ||
| 6-99551877-T-A | not specified | Uncertain significance (Mar 01, 2024) | ||
| 6-99551879-T-C | not specified | Likely benign (Feb 09, 2025) | ||
| 6-99558419-T-TA | CIC-rearranged sarcoma | not provided (-) | ||
| 6-99558500-C-T | not specified | Uncertain significance (Feb 06, 2024) | ||
| 6-99561389-A-C | not specified | Uncertain significance (Jun 17, 2024) | ||
| 6-99561435-A-C | not specified | Uncertain significance (Feb 06, 2024) | ||
| 6-99561603-T-C | not specified | Uncertain significance (Oct 14, 2023) | ||
| 6-99562908-G-A | not specified | Uncertain significance (Jun 10, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CCNC | protein_coding | protein_coding | ENST00000520429 | 12 | 26594 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.999 | 0.000864 | 125235 | 0 | 1 | 125236 | 0.00000399 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.25 | 63 | 137 | 0.459 | 0.00000618 | 1870 |
| Missense in Polyphen | 19 | 47.837 | 0.39718 | 641 | ||
| Synonymous | 0.402 | 42 | 45.4 | 0.924 | 0.00000219 | 467 |
| Loss of Function | 4.19 | 0 | 20.4 | 0.00 | 8.62e-7 | 278 |
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) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000329 | 0.0000329 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Component of the Mediator complex, a coactivator involved in regulated gene transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. Binds to and activates cyclin-dependent kinase CDK8 that phosphorylates the CTD (C-terminal domain) of the large subunit of RNA polymerase II (RNAp II), which may inhibit the formation of a transcription initiation complex. {ECO:0000269|PubMed:16595664, ECO:0000269|PubMed:8700522}.;
- Pathway
- Vitamin D Receptor Pathway;Developmental Biology;Disease;Signal Transduction;Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;Transcriptional regulation of white adipocyte differentiation;SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription;Signaling by NOTCH1;Signaling by NOTCH;Transcriptional activity of SMAD2/SMAD3:SMAD4 heterotrimer;Constitutive Signaling by NOTCH1 PEST Domain Mutants;Signaling by NOTCH1 PEST Domain Mutants in Cancer;Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants;Signaling by NOTCH1 HD+PEST Domain Mutants in Cancer;Signaling by NOTCH1 in Cancer;Signaling by TGF-beta Receptor Complex;Signaling by TGF-beta family members;Diseases of signal transduction;NOTCH1 Intracellular Domain Regulates Transcription
(Consensus)
Recessive Scores
- pRec
- 0.194
Intolerance Scores
- loftool
- 0.537
- rvis_EVS
- -0.1
- rvis_percentile_EVS
- 46.2
Haploinsufficiency Scores
- pHI
- 0.951
- hipred
- Y
- hipred_score
- 0.783
- ghis
- 0.677
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- H
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.967
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Low | Low | Low |
| Primary Immunodeficiency | Low | Low | Low |
| Cancer | Low | Low | Low |
Mouse Genome Informatics
- Gene name
- Ccnc
- 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); neoplasm; embryo phenotype; growth/size/body region phenotype; cellular phenotype;
Zebrafish Information Network
- Gene name
- ccnc
- Affected structure
- pronephric podocyte
- Phenotype tag
- abnormal
- Phenotype quality
- malformed
Gene ontology
- Biological process
- regulation of cyclin-dependent protein serine/threonine kinase activity;regulation of transcription by RNA polymerase II;transcription initiation from RNA polymerase II promoter;protein phosphorylation;positive regulation of transcription by RNA polymerase II
- Cellular component
- nucleus;nucleoplasm;mediator complex
- Molecular function
- protein serine/threonine kinase activity;protein binding;cyclin-dependent protein serine/threonine kinase regulator activity