RAP2B
Basic information
Region (hg38): 3:153162226-153170627
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 RAP2B 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 | 1 | |||||
| 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 | 1 | 0 |
Variants in RAP2B
This is a list of pathogenic ClinVar variants found in the RAP2B region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 3-153162810-T-C | Likely benign (Jun 01, 2020) | |||
| 3-153163090-G-A | not specified | Uncertain significance (Dec 15, 2023) | ||
| 3-153163195-G-T | not specified | Uncertain significance (Feb 22, 2023) | ||
| 3-153163212-T-A | not specified | Uncertain significance (Jul 14, 2023) | ||
| 3-153163226-C-T | not specified | Uncertain significance (May 30, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RAP2B | protein_coding | protein_coding | ENST00000323534 | 1 | 6237 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.487 | 0.494 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.25 | 41 | 106 | 0.385 | 0.00000482 | 1184 |
| Missense in Polyphen | 9 | 51.081 | 0.17619 | 579 | ||
| Synonymous | -0.422 | 54 | 50.2 | 1.08 | 0.00000247 | 367 |
| Loss of Function | 1.87 | 1 | 5.92 | 0.169 | 2.55e-7 | 64 |
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: Small GTP-binding protein which cycles between a GDP- bound inactive and a GTP-bound active form. Involved in EGFR and CHRM3 signaling pathways through stimulation of PLCE1. May play a role in cytoskeletal rearrangements and regulate cell spreading through activation of the effector TNIK. May regulate membrane vesiculation in red blood cells. {ECO:0000269|PubMed:11877431, ECO:0000269|PubMed:15143162, ECO:0000269|PubMed:16540189}.;
- Pathway
- Neutrophil degranulation;phospholipase c-epsilon pathway;Innate Immune System;Immune System
(Consensus)
Recessive Scores
- pRec
- 0.156
Intolerance Scores
- loftool
- 0.113
- rvis_EVS
- -0.03
- rvis_percentile_EVS
- 51.04
Haploinsufficiency Scores
- pHI
- 0.362
- hipred
- Y
- hipred_score
- 0.715
- ghis
- 0.578
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.823
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Medium |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rap2b
- Phenotype
- growth/size/body region phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);
Gene ontology
- Biological process
- signal transduction;microvillus assembly;platelet activation;negative regulation of cell migration;positive regulation of protein autophosphorylation;Rap protein signal transduction;neutrophil degranulation;regulation of protein tyrosine kinase activity;platelet aggregation;establishment of endothelial intestinal barrier
- Cellular component
- cytosol;plasma membrane;bicellular tight junction;membrane;specific granule membrane;cell-cell contact zone;membrane raft;recycling endosome membrane;extracellular exosome;tertiary granule membrane
- Molecular function
- GTPase activity;protein binding;GTP binding;GDP binding;protein domain specific binding