CRB3
Basic information
Region (hg38): 19:6463777-6467221
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 CRB3 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 | 10 | 10 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 10 | 0 | 0 |
Variants in CRB3
This is a list of pathogenic ClinVar variants found in the CRB3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 19-6464723-C-A | not specified | Uncertain significance (Nov 09, 2024) | ||
| 19-6464727-T-C | not specified | Uncertain significance (Jan 17, 2025) | ||
| 19-6464733-C-A | not specified | Uncertain significance (Feb 13, 2025) | ||
| 19-6464745-C-G | not specified | Uncertain significance (Oct 07, 2024) | ||
| 19-6465557-C-T | not specified | Uncertain significance (Apr 23, 2024) | ||
| 19-6465599-C-G | not specified | Uncertain significance (Jul 30, 2024) | ||
| 19-6466472-G-A | not specified | Uncertain significance (Jan 31, 2025) | ||
| 19-6466491-T-A | not specified | Uncertain significance (Apr 18, 2023) | ||
| 19-6466505-C-T | not specified | Uncertain significance (Feb 01, 2025) | ||
| 19-6466547-G-C | not specified | Uncertain significance (Feb 04, 2025) | ||
| 19-6466575-C-T | not specified | Uncertain significance (Aug 14, 2023) | ||
| 19-6466589-C-T | not specified | Uncertain significance (Dec 20, 2023) | ||
| 19-6466976-C-T | not specified | Uncertain significance (Feb 16, 2023) | ||
| 19-6466986-C-G | not specified | Uncertain significance (Sep 23, 2023) | ||
| 19-6467014-C-T | not specified | Uncertain significance (Feb 13, 2025) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CRB3 | protein_coding | protein_coding | ENST00000356762 | 4 | 3445 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.358 | 0.595 | 125525 | 0 | 1 | 125526 | 0.00000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.281 | 59 | 65.4 | 0.902 | 0.00000437 | 760 |
| Missense in Polyphen | 17 | 20.83 | 0.81612 | 204 | ||
| Synonymous | 0.354 | 25 | 27.4 | 0.914 | 0.00000163 | 280 |
| Loss of Function | 1.56 | 1 | 4.60 | 0.217 | 1.97e-7 | 62 |
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) | 0.00000881 | 0.00000881 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in the establishment of cell polarity in mammalian epithelial cells. Regulates the morphogenesis of tight junctions. {ECO:0000269|PubMed:12771187, ECO:0000269|PubMed:14718572}.;
- Pathway
- Tight junction - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);EMT transition in Colorectal Cancer;Tight junction interactions;Cell-cell junction organization;Cell junction organization;Cell-Cell communication
(Consensus)
Recessive Scores
- pRec
- 0.0866
Intolerance Scores
- loftool
- 0.258
- rvis_EVS
- -0.27
- rvis_percentile_EVS
- 33.97
Haploinsufficiency Scores
- pHI
- 0.0889
- hipred
- N
- hipred_score
- 0.261
- ghis
- 0.564
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.127
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Low |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Medium | Low | Medium |
Mouse Genome Informatics
- Gene name
- Crb3
- Phenotype
- homeostasis/metabolism phenotype; cellular phenotype; normal 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); digestive/alimentary phenotype; renal/urinary system phenotype; respiratory system phenotype;
Gene ontology
- Biological process
- bicellular tight junction assembly;protein localization to plasma membrane
- Cellular component
- plasma membrane;bicellular tight junction;integral component of membrane;apical plasma membrane;cell junction;protein-containing complex;extracellular exosome
- Molecular function
- protein binding;SH3 domain binding;protein domain specific binding