CAB39
Basic information
Region (hg38): 2:230712842-230821075
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 CAB39 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 | 3 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 3 | 0 | 0 |
Variants in CAB39
This is a list of pathogenic ClinVar variants found in the CAB39 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 2-230760030-A-G | not specified | Uncertain significance (Mar 26, 2024) | ||
| 2-230790905-A-G | not specified | Uncertain significance (Feb 21, 2024) | ||
| 2-230818541-C-T | not specified | Uncertain significance (Feb 06, 2024) | ||
| 2-230818587-A-G | not specified | Uncertain significance (Dec 28, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CAB39 | protein_coding | protein_coding | ENST00000258418 | 8 | 108231 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0680 | 0.929 | 125732 | 0 | 7 | 125739 | 0.0000278 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.38 | 86 | 175 | 0.493 | 0.00000867 | 2286 |
| Missense in Polyphen | 20 | 52.118 | 0.38374 | 757 | ||
| Synonymous | 1.17 | 54 | 66.1 | 0.816 | 0.00000390 | 589 |
| Loss of Function | 2.64 | 5 | 16.6 | 0.301 | 7.83e-7 | 227 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000293 | 0.0000293 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000552 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000367 | 0.0000352 |
| Middle Eastern | 0.0000552 | 0.0000544 |
| South Asian | 0.0000455 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Component of a complex that binds and activates STK11/LKB1. In the complex, required to stabilize the interaction between CAB39/MO25 (CAB39/MO25alpha or CAB39L/MO25beta) and STK11/LKB1. {ECO:0000269|PubMed:19892943}.;
- Pathway
- mTOR signaling pathway - Homo sapiens (human);AMPK signaling pathway - Homo sapiens (human);AMP-activated Protein Kinase (AMPK) Signaling;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;Endochondral Ossification;Neutrophil degranulation;Signal Transduction;Energy dependent regulation of mTOR by LKB1-AMPK;mTOR signalling;Innate Immune System;Immune System;LKB1 signaling events
(Consensus)
Recessive Scores
- pRec
- 0.118
Intolerance Scores
- loftool
- 0.693
- rvis_EVS
- -0.05
- rvis_percentile_EVS
- 49.76
Haploinsufficiency Scores
- pHI
- 0.653
- hipred
- Y
- hipred_score
- 0.798
- ghis
- 0.572
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.903
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cab39
- Phenotype
Gene ontology
- Biological process
- cell cycle arrest;positive regulation of peptidyl-threonine phosphorylation;peptidyl-serine phosphorylation;signal transduction by protein phosphorylation;activation of protein kinase activity;intracellular signal transduction;neutrophil degranulation;protein heterooligomerization;cellular hypotonic response;positive regulation of protein serine/threonine kinase activity;negative regulation of potassium ion transmembrane transporter activity;negative regulation of potassium ion transmembrane transport
- Cellular component
- extracellular region;cytosol;secretory granule lumen;extracellular exosome;serine/threonine protein kinase complex;ficolin-1-rich granule lumen
- Molecular function
- protein serine/threonine kinase activity;protein binding;kinase binding;protein kinase activator activity;protein serine/threonine kinase activator activity