CBLL1
Basic information
Region (hg38): 7:107743073-107761667
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (34 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CBLL1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000024814.4. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 34 | 34 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 34 | 0 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CBLL1 | protein_coding | protein_coding | ENST00000440859 | 6 | 17971 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.999 | 0.000822 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.34 | 222 | 286 | 0.777 | 0.0000147 | 3228 |
| Missense in Polyphen | 50 | 97.642 | 0.51208 | 1122 | ||
| Synonymous | -1.56 | 109 | 90.1 | 1.21 | 0.00000464 | 975 |
| Loss of Function | 4.20 | 0 | 20.5 | 0.00 | 0.00000141 | 219 |
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 | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: E3 ubiquitin-protein ligase that mediates ubiquitination of several tyrosine-phosphorylated Src substrates, including CDH1, CTTN and DOK1 (By similarity). Targets CDH1 for endocytosis and degradation (By similarity). Associated component of the WMM complex, a complex that mediates N6-methyladenosine (m6A) methylation of RNAs, a modification that plays a role in the efficiency of mRNA splicing and RNA processing (PubMed:29507755). Its function in the WMM complex is unknown (PubMed:29507755). {ECO:0000250|UniProtKB:Q9JIY2, ECO:0000269|PubMed:29507755}.;
- Pathway
- Disease;Infectious disease;Posttranslational regulation of adherens junction stability and dissassembly;InlA-mediated entry of Listeria monocytogenes into host cells;Listeria monocytogenes entry into host cells
(Consensus)
Recessive Scores
- pRec
- 0.110
Intolerance Scores
- loftool
- rvis_EVS
- -0.52
- rvis_percentile_EVS
- 21.2
Haploinsufficiency Scores
- pHI
- 0.293
- hipred
- Y
- hipred_score
- 0.788
- ghis
- 0.664
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- H
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.974
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cbll1
- Phenotype
Gene ontology
- Biological process
- negative regulation of cell adhesion;multicellular organism development;protein ubiquitination;positive regulation of cell migration;entry of bacterium into host cell;positive regulation of endocytosis;mRNA methylation;cell-cell adhesion
- Cellular component
- ubiquitin ligase complex;cytoplasm;cytosol;nuclear speck;RNA N6-methyladenosine methyltransferase complex
- Molecular function
- ubiquitin-protein transferase activity;protein binding;identical protein binding;metal ion binding;ubiquitin protein ligase activity