RAP2C
Basic information
Region (hg38): X:132203024-132219480
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 RAP2C 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 | 2 | |||||
| missense | 1 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 1 | 1 | 1 |
Variants in RAP2C
This is a list of pathogenic ClinVar variants found in the RAP2C region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| X-132214186-T-G | Benign (Dec 14, 2018) | |||
| X-132214200-C-A | not specified | Uncertain significance (Feb 05, 2024) | ||
| X-132214402-A-G | Likely benign (Apr 16, 2018) | |||
| X-132217028-C-T | not specified | Uncertain significance (May 20, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RAP2C | protein_coding | protein_coding | ENST00000342983 | 2 | 16419 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.296 | 0.631 | 124648 | 0 | 1 | 124649 | 0.00000401 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.73 | 23 | 61.0 | 0.377 | 0.00000416 | 1196 |
| Missense in Polyphen | 7 | 21.825 | 0.32073 | 467 | ||
| Synonymous | -1.07 | 31 | 24.3 | 1.28 | 0.00000182 | 356 |
| Loss of Function | 1.37 | 1 | 3.94 | 0.254 | 2.47e-7 | 91 |
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) | 0.0000123 | 0.00000889 |
| 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. May play a role in cytoskeletal rearrangements and regulate cell spreading through activation of the effector TNIK. May play a role in SRE-mediated gene transcription. {ECO:0000269|PubMed:17447155}.;
- Pathway
- Tight junction - Homo sapiens (human);Neutrophil degranulation;Innate Immune System;Immune System
(Consensus)
Recessive Scores
- pRec
- 0.136
Intolerance Scores
- loftool
- 0.177
- rvis_EVS
- -0.01
- rvis_percentile_EVS
- 52.85
Haploinsufficiency Scores
- pHI
- 0.612
- hipred
- N
- hipred_score
- 0.483
- ghis
- 0.593
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Low | Low | Low |
| Primary Immunodeficiency | Low | Low | Low |
| Cancer | Low | Low | Low |
Mouse Genome Informatics
- Gene name
- Rap2c
- Phenotype
Gene ontology
- Biological process
- microvillus assembly;negative regulation of cell migration;positive regulation of protein autophosphorylation;Rap protein signal transduction;neutrophil degranulation;regulation of protein tyrosine kinase activity;establishment of endothelial intestinal barrier;positive regulation of nucleic acid-templated transcription
- Cellular component
- cytoplasm;cytosol;plasma membrane;bicellular tight junction;cell-cell contact zone;recycling endosome membrane;extracellular exosome;tertiary granule membrane
- Molecular function
- transcription coactivator activity;GTPase activity;protein binding;GTP binding;GDP binding