RAPGEF5
Basic information
Region (hg38): 7:22118236-22357154
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (64 variants)
- not_provided (2 variants)
- Dilated_cardiomyopathy_1A (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAPGEF5 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000012294.5. 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 | 62 | 66 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 1 | 62 | 3 | 0 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
RAPGEF5 | protein_coding | protein_coding | ENST00000344041 | 23 | 238908 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.981 | 0.0190 | 124626 | 0 | 10 | 124636 | 0.0000401 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.64 | 276 | 364 | 0.759 | 0.0000186 | 4799 |
Missense in Polyphen | 94 | 144.4 | 0.65096 | 2003 | ||
Synonymous | 0.224 | 131 | 134 | 0.975 | 0.00000734 | 1266 |
Loss of Function | 5.30 | 8 | 47.4 | 0.169 | 0.00000251 | 574 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000203 | 0.000203 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.0000684 | 0.0000556 |
Finnish | 0.0000466 | 0.0000464 |
European (Non-Finnish) | 0.0000178 | 0.0000177 |
Middle Eastern | 0.0000684 | 0.0000556 |
South Asian | 0.00 | 0.00 |
Other | 0.000169 | 0.000165 |
dbNSFP
Source:
- Function
- FUNCTION: Guanine nucleotide exchange factor (GEF) for RAP1A, RAP2A and MRAS/M-Ras-GTP. Its association with MRAS inhibits Rap1 activation. {ECO:0000269|PubMed:10777494, ECO:0000269|PubMed:10934204}.;
- Pathway
- Rap1 signaling pathway - Homo sapiens (human);Ras signaling pathway - Homo sapiens (human);Pathways in clear cell renal cell carcinoma;Ras Signaling
(Consensus)
Recessive Scores
- pRec
- 0.0809
Intolerance Scores
- loftool
- 0.526
- rvis_EVS
- -0.98
- rvis_percentile_EVS
- 8.8
Haploinsufficiency Scores
- pHI
- 0.112
- hipred
- Y
- hipred_score
- 0.819
- ghis
- 0.522
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.788
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rapgef5
- Phenotype
Gene ontology
- Biological process
- small GTPase mediated signal transduction;nervous system development
- Cellular component
- nucleus;nucleoplasm;nuclear body
- Molecular function
- Ras guanyl-nucleotide exchange factor activity;Rap guanyl-nucleotide exchange factor activity;GTP-dependent protein binding