RAB38

RAB38, member RAS oncogene family, the group of RAB, member RAS oncogene GTPases

Basic information

Region (hg38): 11:88113250-88175443

Links

ENSG00000123892 ∙ NCBI:23682 ∙ OMIM:606281 ∙ HGNC:9776 ∙ Uniprot:P57729 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RAB38 gene.

• Inborn genetic diseases (8 variants)

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			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	0	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)

GnomAD

Source: gnomAD

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: dbNSFP

• 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