CNN3
Basic information
Region (hg38): 1:94896948-94927223
Links
Phenotypes
GenCC
Source:
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 CNN3 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 CNN3
This is a list of pathogenic ClinVar variants found in the CNN3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-94897774-A-G | not specified | Uncertain significance (Nov 09, 2021) | ||
| 1-94897801-C-T | not specified | Uncertain significance (Feb 23, 2023) | ||
| 1-94897924-G-A | not specified | Uncertain significance (Mar 19, 2024) | ||
| 1-94897929-T-C | not specified | Uncertain significance (Jan 03, 2024) | ||
| 1-94898044-C-T | not specified | Uncertain significance (Jan 08, 2024) | ||
| 1-94898074-A-C | not specified | Uncertain significance (Oct 05, 2023) | ||
| 1-94899432-T-C | not specified | Uncertain significance (May 23, 2023) | ||
| 1-94901686-T-C | not specified | Uncertain significance (Mar 24, 2023) | ||
| 1-94902213-T-C | not specified | Uncertain significance (Jun 27, 2023) | ||
| 1-94926849-C-T | not specified | Uncertain significance (Apr 20, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CNN3 | protein_coding | protein_coding | ENST00000370206 | 7 | 30328 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.599 | 0.401 | 125741 | 0 | 7 | 125748 | 0.0000278 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.24 | 95 | 180 | 0.529 | 0.00000896 | 2182 |
| Missense in Polyphen | 19 | 52.233 | 0.36376 | 691 | ||
| Synonymous | 1.93 | 45 | 64.7 | 0.696 | 0.00000359 | 601 |
| Loss of Function | 2.99 | 3 | 15.8 | 0.189 | 6.77e-7 | 199 |
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) | 0.0000624 | 0.0000615 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Thin filament-associated protein that is implicated in the regulation and modulation of smooth muscle contraction. It is capable of binding to actin, calmodulin, troponin C and tropomyosin. The interaction of calponin with actin inhibits the actomyosin Mg-ATPase activity.;
Recessive Scores
- pRec
- 0.138
Intolerance Scores
- loftool
- 0.437
- rvis_EVS
- 0.3
- rvis_percentile_EVS
- 72.01
Haploinsufficiency Scores
- pHI
- 0.467
- hipred
- Y
- hipred_score
- 0.693
- ghis
- 0.439
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.735
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cnn3
- 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); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan);
Gene ontology
- Biological process
- epithelial cell differentiation;actomyosin structure organization;negative regulation of ATPase activity;cell-cell adhesion
- Cellular component
- cytosol;cell-cell adherens junction;focal adhesion;postsynaptic density;actin cytoskeleton;neuronal cell body;dendritic spine
- Molecular function
- actin binding;calmodulin binding;microtubule binding;cadherin binding involved in cell-cell adhesion