RAB12
Basic information
Region (hg38): 18:8609437-8639383
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 RAB12 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 | 10 | 10 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 0 | |||||
| Total | 0 | 0 | 10 | 1 | 0 |
Variants in RAB12
This is a list of pathogenic ClinVar variants found in the RAB12 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 18-8609750-A-C | not specified | Uncertain significance (Oct 06, 2021) | ||
| 18-8609762-G-C | not specified | Uncertain significance (Jan 06, 2023) | ||
| 18-8609764-G-A | not specified | Uncertain significance (Apr 25, 2022) | ||
| 18-8609776-C-G | not specified | Uncertain significance (Sep 20, 2023) | ||
| 18-8609791-C-T | task-specific movement disorders • not specified | Uncertain significance (Aug 17, 2021) | ||
| 18-8609794-G-T | not specified | Uncertain significance (Dec 20, 2023) | ||
| 18-8609813-G-T | not specified | Uncertain significance (Apr 01, 2024) | ||
| 18-8609840-C-T | not specified | Uncertain significance (Sep 14, 2022) | ||
| 18-8624987-A-G | RAB12-related disorder | Likely benign (Sep 25, 2019) | ||
| 18-8635613-G-T | not specified | Uncertain significance (Mar 01, 2023) | ||
| 18-8638143-C-T | RAB12-related disorder | Likely benign (Oct 28, 2019) | ||
| 18-8638183-A-G | not specified | Uncertain significance (Oct 03, 2022) | ||
| 18-8638218-C-T | not specified | Uncertain significance (Apr 18, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RAB12 | protein_coding | protein_coding | ENST00000329286 | 6 | 29937 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0428 | 0.932 | 124754 | 0 | 25 | 124779 | 0.000100 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.69 | 70 | 123 | 0.570 | 0.00000598 | 1595 |
| Missense in Polyphen | 12 | 35.342 | 0.33954 | 450 | ||
| Synonymous | -1.11 | 57 | 47.3 | 1.21 | 0.00000249 | 458 |
| Loss of Function | 1.95 | 4 | 10.9 | 0.365 | 4.60e-7 | 149 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00110 | 0.00107 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000179 | 0.000111 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000284 | 0.0000177 |
| Middle Eastern | 0.000179 | 0.000111 |
| South Asian | 0.0000743 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: The small GTPases Rab are key regulators of intracellular membrane trafficking, from the formation of transport vesicles to their fusion with membranes. Rabs cycle between an inactive GDP-bound form and an active GTP-bound form that is able to recruit to membranes different set of downstream effectors directly responsible for vesicle formation, movement, tethering and fusion. That Rab may play a role in protein transport from recycling endosomes to lysosomes regulating, for instance, the degradation of the transferrin receptor. Involved in autophagy (By similarity). {ECO:0000250}.;
- Pathway
- Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Rab regulation of trafficking;RAB GEFs exchange GTP for GDP on RABs;RAB geranylgeranylation
(Consensus)
Intolerance Scores
- loftool
- 0.106
- rvis_EVS
- -0.21
- rvis_percentile_EVS
- 38.28
Haploinsufficiency Scores
- pHI
- 0.159
- hipred
- Y
- hipred_score
- 0.728
- ghis
- 0.649
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.508
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rab12
- Phenotype
Gene ontology
- Biological process
- intracellular protein transport;endoplasmic reticulum to Golgi vesicle-mediated transport;autophagy;endosome to lysosome transport;positive regulation of macroautophagy;Rab protein signal transduction;cellular protein catabolic process;cellular response to interferon-gamma
- Cellular component
- Golgi membrane;lysosome;lysosomal membrane;autophagosome;endoplasmic reticulum membrane;trans-Golgi network;cytosol;phagocytic vesicle;recycling endosome membrane
- Molecular function
- GTPase activity;protein binding;GTP binding;GDP binding