RAB25

RAB25, member RAS oncogene family, the group of RAB, member RAS oncogene GTPases

Basic information

Region (hg38): 1:156061160-156070504

Links

ENSG00000132698 ∙ NCBI:57111 ∙ OMIM:612942 ∙ HGNC:18238 ∙ Uniprot:P57735 ∙ 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 RAB25 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAB25 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			17	1		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	1	0

Variants in RAB25

This is a list of pathogenic ClinVar variants found in the RAB25 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-156061405-G-A		not specified	Uncertain significance (Feb 05, 2024)
1-156061419-G-A		not specified	Uncertain significance (Jan 08, 2024)
1-156061426-A-G		not specified	Uncertain significance (Apr 27, 2023)
1-156065911-T-C		not specified	Uncertain significance (Jun 04, 2024)
1-156065926-A-G			Likely benign (Apr 01, 2024)
1-156065973-G-A		not specified	Uncertain significance (Jan 23, 2023)
1-156066019-C-T		not specified	Uncertain significance (Nov 07, 2022)
1-156066022-G-A		not specified	Uncertain significance (Jul 27, 2022)
1-156066091-G-A		not specified	Uncertain significance (Feb 06, 2024)
1-156066103-C-G		not specified	Uncertain significance (Oct 26, 2022)
1-156066103-C-T		not specified	Uncertain significance (Jun 07, 2024)
1-156068302-T-G		not specified	Uncertain significance (Nov 15, 2021)
1-156068380-C-T		not specified	Uncertain significance (Nov 08, 2021)
1-156068382-A-T		not specified	Uncertain significance (Mar 18, 2024)
1-156068428-G-A		not specified	Uncertain significance (Mar 25, 2022)
1-156068448-G-T		not specified	Uncertain significance (Dec 27, 2022)
1-156069688-T-C		not specified	Uncertain significance (Jul 27, 2021)
1-156069738-G-C		not specified	Uncertain significance (Jan 24, 2024)
1-156070169-C-A		not specified	Uncertain significance (Jun 21, 2023)
1-156070181-A-G		not specified	Uncertain significance (May 05, 2023)
1-156070189-C-G		not specified	Uncertain significance (Jan 04, 2024)
1-156070234-G-C		not specified	Uncertain significance (Apr 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAB25	protein_coding	protein_coding	ENST00000361084	5	9345

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.12e-7	0.196	124457	0	372	124829	0.00149

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.815	106	132	0.801	0.00000800	1367
Missense in Polyphen		55	62.08	0.88596		606
Synonymous	0.0632	54	54.6	0.989	0.00000320	448
Loss of Function	0.168	11	11.6	0.947	8.26e-7	106

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00197	0.00197
Ashkenazi Jewish	0.00	0.00
East Asian	0.000223	0.000222
Finnish	0.00163	0.00162
European (Non-Finnish)	0.00237	0.00234
Middle Eastern	0.000223	0.000222
South Asian	0.000268	0.000261
Other	0.000331	0.000329

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the regulation of cell survival. Promotes invasive migration of cells in which it functions to localize and maintain integrin alpha-V/beta-1 at the tips of extending pseudopodia (PubMed:17925226). Involved in the regulation of epithelial morphogenesis through the control of CLDN4 expression and localization at tight junctions (By similarity). May selectively regulate the apical recycling pathway. Together with MYO5B regulates transcytosis (By similarity). {ECO:0000250|UniProtKB:E2RQ15, ECO:0000250|UniProtKB:P46629, ECO:0000250|UniProtKB:Q9WTL2, ECO:0000269|PubMed:17925226}.
• Pathway: Post-translational protein modification;Metabolism of proteins;RAB geranylgeranylation (Consensus)

Recessive Scores

• pRec: 0.0925

Intolerance Scores

• loftool: 0.600
• rvis_EVS: 0.35
• rvis_percentile_EVS: 74.18

Haploinsufficiency Scores

• pHI: 0.214
• hipred: N
• hipred_score: 0.251
• ghis: 0.492

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.801

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Rab25
• Phenotype: neoplasm; reproductive system phenotype; digestive/alimentary phenotype

Gene ontology

• Biological process: epithelial cell morphogenesis;intracellular protein transport;exocytosis;positive regulation of cell population proliferation;positive regulation of epithelial cell migration;pseudopodium organization;Rab protein signal transduction;regulation of vesicle-mediated transport
• Cellular component: endosome;pseudopodium;pseudopodium membrane;cytoplasmic vesicle;recycling endosome;extracellular exosome
• Molecular function: GTPase activity;protein binding;GTP binding;myosin V binding