RABIF
Basic information
Region (hg38): 1:202878282-202889149
Previous symbols: [ "RASGRF3" ]
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 RABIF 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 | 0 | 1 |
Variants in RABIF
This is a list of pathogenic ClinVar variants found in the RABIF region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-202881009-T-C | not specified | Uncertain significance (Dec 12, 2023) | ||
| 1-202881067-C-T | not specified | Uncertain significance (May 29, 2024) | ||
| 1-202881084-A-G | not specified | Uncertain significance (Mar 27, 2023) | ||
| 1-202881095-G-A | Benign (Jul 10, 2017) | |||
| 1-202888998-C-T | not specified | Uncertain significance (Apr 08, 2024) | ||
| 1-202889080-G-C | not specified | Uncertain significance (Dec 01, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RABIF | protein_coding | protein_coding | ENST00000367262 | 2 | 10179 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0144 | 0.696 | 125735 | 0 | 13 | 125748 | 0.0000517 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.0688 | 71 | 69.4 | 1.02 | 0.00000347 | 796 |
| Missense in Polyphen | 19 | 26.525 | 0.7163 | 294 | ||
| Synonymous | -1.66 | 40 | 28.7 | 1.39 | 0.00000162 | 245 |
| Loss of Function | 0.620 | 3 | 4.40 | 0.681 | 1.95e-7 | 47 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000563 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000622 | 0.0000615 |
| Middle Eastern | 0.0000563 | 0.0000544 |
| South Asian | 0.000166 | 0.000163 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Guanine-nucleotide-releasing protein that acts on members of the SEC4/YPT1/RAB subfamily. Stimulates GDP release from both YPT1 and RAB3A, but is less active on these proteins than on the SEC4 protein. Might play a general role in vesicular transport.;
- Pathway
- Retinoblastoma (RB) in Cancer
(Consensus)
Recessive Scores
- pRec
- 0.128
Intolerance Scores
- loftool
- 0.354
- rvis_EVS
- -0.01
- rvis_percentile_EVS
- 53.19
Haploinsufficiency Scores
- pHI
- 0.156
- hipred
- N
- hipred_score
- 0.325
- ghis
- 0.514
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.820
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rabif
- Phenotype
Gene ontology
- Biological process
- post-Golgi vesicle-mediated transport;small GTPase mediated signal transduction;protein transport;membrane fusion
- Cellular component
- cytosol;membrane
- Molecular function
- guanyl-nucleotide exchange factor activity;protein binding;zinc ion binding