RAB15

RAB15, member RAS oncogene family, the group of RAB, member RAS oncogene GTPases

Basic information

Region (hg38): 14:64945813-64973226

Links

ENSG00000139998 ∙ NCBI:376267 ∙ OMIM:619547 ∙ HGNC:20150 ∙ Uniprot:P59190 ∙ 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 RAB15 gene.

• Inborn genetic diseases (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAB15 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			3	1		4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	1	0

Variants in RAB15

This is a list of pathogenic ClinVar variants found in the RAB15 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-64948678-T-C		not specified	Uncertain significance (Dec 27, 2023)
14-64950412-G-A		not specified	Likely benign (Sep 16, 2021)
14-64951051-G-A		not specified	Likely benign (Nov 22, 2023)
14-64951082-C-T		not specified	Uncertain significance (Jan 24, 2024)
14-64951099-A-G		not specified	Uncertain significance (May 17, 2023)
14-64971977-G-A		not specified	Uncertain significance (Jan 23, 2024)
14-64971998-G-C		not specified	Uncertain significance (Aug 12, 2021)
14-64972058-C-T		not specified	Uncertain significance (Feb 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAB15	protein_coding	protein_coding	ENST00000267512	7	26963

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00596	0.975	125740	0	5	125745	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.16	89	125	0.710	0.00000711	1344
Missense in Polyphen		14	31.219	0.44844		351
Synonymous	0.609	43	48.4	0.889	0.00000295	392
Loss of Function	2.05	6	14.4	0.417	7.82e-7	145

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000452	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act in concert with RAB3A in regulating aspects of synaptic vesicle membrane flow within the nerve terminal. {ECO:0000250}.
• Pathway: Post-translational protein modification;Metabolism of proteins;RAB geranylgeranylation (Consensus)

Intolerance Scores

• loftool: 0.539
• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.95

Haploinsufficiency Scores

• pHI: 0.141
• hipred: N
• hipred_score: 0.238
• ghis: 0.565

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rab15
• Phenotype: pigmentation phenotype; vision/eye phenotype; skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: intracellular protein transport;vesicle docking involved in exocytosis;protein secretion;regulation of exocytosis;Rab protein signal transduction;protein localization to plasma membrane;positive regulation of regulated secretory pathway
• Cellular component: cytoplasm;endosome;plasma membrane;cilium;synaptic vesicle;endosome membrane;perinuclear region of cytoplasm;extracellular exosome
• Molecular function: GTPase activity;protein binding;GTP binding