RAB18
Basic information
Region (hg38): 10:27504174-27545117
Links
Phenotypes
GenCC
Source:
- Warburg micro syndrome 3 (Definitive), mode of inheritance: AR
- Warburg micro syndrome 3 (Strong), mode of inheritance: AR
- Warburg micro syndrome (Supportive), mode of inheritance: AR
- Warburg micro syndrome (Moderate), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Warburg micro syndrome 3 | AR | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Craniofacial; Musculoskeletal; Neurologic; Ophthalmologic | 21473985 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (43 variants)
- Inborn_genetic_diseases (22 variants)
- Warburg_micro_syndrome_3 (19 variants)
- RAB18-related_disorder (8 variants)
- not_specified (8 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAB18 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000021252.5. 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 | 15 | 16 | ||||
missense | 32 | 38 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 4 | |||||
splice donor/acceptor (+/-2bp) | 1 | |||||
Total | 3 | 3 | 35 | 17 | 1 |
Highest pathogenic variant AF is 0.00000805922
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
RAB18 | protein_coding | protein_coding | ENST00000356940 | 7 | 37947 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.910 | 0.0898 | 125697 | 0 | 6 | 125703 | 0.0000239 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.39 | 68 | 109 | 0.625 | 0.00000511 | 1342 |
Missense in Polyphen | 25 | 42.709 | 0.58536 | 539 | ||
Synonymous | -0.297 | 42 | 39.6 | 1.06 | 0.00000198 | 382 |
Loss of Function | 2.96 | 1 | 12.2 | 0.0823 | 6.10e-7 | 147 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000123 | 0.000123 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.0000544 | 0.0000544 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000264 | 0.0000264 |
Middle Eastern | 0.0000544 | 0.0000544 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Plays a role in apical endocytosis/recycling. May be implicated in transport between the plasma membrane and early endosomes. Plays a key role in eye and brain development and neurodegeneration. {ECO:0000269|PubMed:21473985}.;
- Pathway
- Neutrophil degranulation;Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Innate Immune System;Immune System;Rab regulation of trafficking;COPI-independent Golgi-to-ER retrograde traffic;Golgi-to-ER retrograde transport;RAB GEFs exchange GTP for GDP on RABs;RAB geranylgeranylation;Intra-Golgi and retrograde Golgi-to-ER traffic
(Consensus)
Recessive Scores
- pRec
- 0.110
Intolerance Scores
- loftool
- 0.541
- rvis_EVS
- 0.1
- rvis_percentile_EVS
- 61.28
Haploinsufficiency Scores
- pHI
- 0.192
- hipred
- Y
- hipred_score
- 0.580
- ghis
- 0.564
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- H
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.961
Mouse Genome Informatics
- Gene name
- Rab18
- Phenotype
- cellular phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype;
Zebrafish Information Network
- Gene name
- rab18b
- Affected structure
- iridophore
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- eye development;intracellular protein transport;small GTPase mediated signal transduction;brain development;Rab protein signal transduction;lipid droplet organization;neutrophil degranulation;import into nucleus;endoplasmic reticulum tubular network organization
- Cellular component
- endoplasmic reticulum membrane;Golgi apparatus;cytosol;plasma membrane;secretory granule membrane;synapse;endoplasmic reticulum tubular network
- Molecular function
- GTPase activity;protein binding;GTP binding;GDP binding