COTL1
Basic information
Region (hg38): 16:84565596-84618078
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 COTL1 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 | 8 | 0 | 0 |
Variants in COTL1
This is a list of pathogenic ClinVar variants found in the COTL1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 16-84566852-G-A | not specified | Uncertain significance (Dec 14, 2022) | ||
| 16-84566904-A-T | not specified | Uncertain significance (Jun 10, 2022) | ||
| 16-84566925-G-A | not specified | Uncertain significance (Jun 05, 2023) | ||
| 16-84590140-C-T | not specified | Uncertain significance (Apr 26, 2023) | ||
| 16-84590161-C-T | not specified | Uncertain significance (May 31, 2023) | ||
| 16-84590235-C-A | not specified | Uncertain significance (Nov 24, 2024) | ||
| 16-84590245-C-A | not specified | Uncertain significance (Mar 01, 2023) | ||
| 16-84590253-C-T | not specified | Uncertain significance (Oct 05, 2023) | ||
| 16-84590257-C-T | not specified | Uncertain significance (Dec 08, 2023) | ||
| 16-84617578-G-C | not specified | Uncertain significance (Nov 24, 2024) | ||
| 16-84617870-G-T | not specified | Uncertain significance (Aug 14, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| COTL1 | protein_coding | protein_coding | ENST00000262428 | 4 | 52484 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0391 | 0.849 | 125410 | 0 | 4 | 125414 | 0.0000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.125 | 101 | 97.5 | 1.04 | 0.00000636 | 922 |
| Missense in Polyphen | 23 | 30.94 | 0.74338 | 300 | ||
| Synonymous | -1.50 | 56 | 43.4 | 1.29 | 0.00000328 | 261 |
| Loss of Function | 1.28 | 3 | 6.55 | 0.458 | 2.77e-7 | 76 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000116 | 0.000116 |
| 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 | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Binds to F-actin in a calcium-independent manner. Has no direct effect on actin depolymerization. Acts as a chaperone for ALOX5 (5LO), influencing both its stability and activity in leukotrienes synthesis. {ECO:0000269|PubMed:11583571, ECO:0000269|PubMed:19807693}.;
- Pathway
- Neutrophil degranulation;Innate Immune System;Immune System
(Consensus)
Recessive Scores
- pRec
- 0.145
Intolerance Scores
- loftool
- 0.281
- rvis_EVS
- -0.23
- rvis_percentile_EVS
- 36.86
Haploinsufficiency Scores
- pHI
- 0.216
- hipred
- Y
- hipred_score
- 0.582
- ghis
- 0.632
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.781
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cotl1
- 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); vision/eye phenotype; pigmentation phenotype;
Gene ontology
- Biological process
- biological_process;neutrophil degranulation;defense response to fungus
- Cellular component
- extracellular region;nucleus;cytoskeleton;secretory granule lumen;extracellular exosome;ficolin-1-rich granule lumen
- Molecular function
- actin binding;protein binding;enzyme binding