RAB38
RAB38, member RAS oncogene family, the group of RAB, member RAS oncogene GTPases
Basic information
Region (hg38): 11:88113251-88175443
Links
Phenotypes
GenCC
Source:
No genCC data.
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 RAB38 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 | 0 | |||||
| missense | 11 | 12 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 11 | 1 | 0 |
Variants in RAB38
This is a list of pathogenic ClinVar variants found in the RAB38 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 11-88114014-T-C | not specified | Uncertain significance (Jun 27, 2022) | ||
| 11-88114047-C-T | not specified | Uncertain significance (Aug 02, 2022) | ||
| 11-88114050-C-T | not specified | Likely benign (Feb 02, 2024) | ||
| 11-88114067-T-C | not specified | Uncertain significance (Nov 29, 2023) | ||
| 11-88114118-G-C | not specified | Uncertain significance (May 03, 2023) | ||
| 11-88114130-T-C | not specified | Uncertain significance (Feb 14, 2023) | ||
| 11-88114133-A-G | not specified | Uncertain significance (Nov 15, 2023) | ||
| 11-88149682-G-A | not specified | Uncertain significance (Jul 05, 2023) | ||
| 11-88149708-G-C | not specified | Uncertain significance (Mar 02, 2023) | ||
| 11-88149745-T-G | not specified | Uncertain significance (May 24, 2023) | ||
| 11-88149917-G-C | not specified | Uncertain significance (Apr 26, 2023) | ||
| 11-88175251-T-C | not specified | Uncertain significance (Jan 30, 2024) | ||
| 11-88175371-T-C | not specified | Uncertain significance (Jun 18, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RAB38 | protein_coding | protein_coding | ENST00000243662 | 3 | 62226 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00197 | 0.751 | 125734 | 0 | 14 | 125748 | 0.0000557 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.157 | 126 | 121 | 1.04 | 0.00000604 | 1392 |
| Missense in Polyphen | 63 | 58.377 | 1.0792 | 673 | ||
| Synonymous | 0.736 | 44 | 50.7 | 0.869 | 0.00000288 | 402 |
| Loss of Function | 0.903 | 5 | 7.70 | 0.649 | 4.12e-7 | 91 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000145 | 0.000145 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.0000532 | 0.0000527 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.000173 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: May be involved in melanosomal transport and docking. Involved in the proper sorting of TYRP1. Involved in peripheral melanosomal distribution of TYRP1 in melanocytes; the function, which probably is implicating vesicle-trafficking, includes cooperation with ANKRD27 and VAMP7 (By similarity). Plays a role in the maturation of phagosomes that engulf pathogens, such as S.aureus and M.tuberculosis (PubMed:21255211). Plays an important role in the control of melanin production and melanosome biogenesis (PubMed:23084991). In concert with RAB32, regulates the proper trafficking of melanogenic enzymes TYR, TYRP1 and DCT/TYRP2 to melanosomes in melanocytes (By similarity). {ECO:0000250|UniProtKB:Q8QZZ8, ECO:0000269|PubMed:21255211, ECO:0000269|PubMed:23084991}.;
- Pathway
- Endoderm Differentiation;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;Validated transcriptional targets of deltaNp63 isoforms
(Consensus)
Recessive Scores
- pRec
- 0.146
Intolerance Scores
- loftool
- 0.538
- rvis_EVS
- 0.31
- rvis_percentile_EVS
- 72.23
Haploinsufficiency Scores
- pHI
- 0.250
- hipred
- N
- hipred_score
- 0.398
- ghis
- 0.501
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.357
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rab38
- 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); respiratory system phenotype; pigmentation phenotype; vision/eye phenotype;
Gene ontology
- Biological process
- intracellular protein transport;mitochondrion organization;small GTPase mediated signal transduction;protein transport;vesicle-mediated transport;Rab protein signal transduction;endosome to melanosome transport;post-translational protein modification;platelet dense granule organization;protein localization to membrane;phagosome acidification;melanosome assembly;positive regulation of phosphatidylcholine biosynthetic process
- Cellular component
- mitochondrion;lysosome;early endosome;endoplasmic reticulum;trans-Golgi network;cytosol;plasma membrane;membrane;phagocytic vesicle membrane;early endosome lumen;melanosome membrane;melanosome;mitochondria-associated endoplasmic reticulum membrane;phagocytic vesicle
- Molecular function
- GTPase activity;protein binding;GTP binding;GTP-dependent protein binding;AP-2 adaptor complex binding;AP-1 adaptor complex binding;AP-3 adaptor complex binding;BLOC-2 complex binding