RAB3B

RAB3B, member RAS oncogene family, the group of RAB, member RAS oncogene GTPases

Basic information

Region (hg38): 1:51907956-51990700

Links

ENSG00000169213 ∙ NCBI:5865 ∙ OMIM:179510 ∙ HGNC:9778 ∙ Uniprot:P20337 ∙ 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 RAB3B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAB3B 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			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	0	0

Variants in RAB3B

This is a list of pathogenic ClinVar variants found in the RAB3B region.

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

Position	Type	Phenotype	Significance	ClinVar
1-51919976-G-A		not specified	Uncertain significance (Apr 12, 2022)
1-51920030-T-C		not specified	Uncertain significance (Dec 14, 2023)
1-51920040-T-C		not specified	Uncertain significance (Feb 07, 2023)
1-51920055-G-A		not specified	Uncertain significance (Dec 28, 2023)
1-51920058-C-T		not specified	Uncertain significance (Feb 08, 2023)
1-51920091-C-T		not specified	Uncertain significance (Oct 31, 2023)
1-51920104-G-T		not specified	Uncertain significance (Jun 11, 2021)
1-51933419-G-A		not specified	Uncertain significance (Mar 28, 2023)
1-51933441-C-A		not specified	Uncertain significance (Jan 24, 2024)
1-51937331-T-C		not specified	Uncertain significance (Oct 10, 2023)
1-51937379-T-C		not specified	Uncertain significance (Dec 17, 2023)
1-51937387-C-T		not specified	Uncertain significance (Jan 10, 2022)
1-51976922-G-A		not specified	Uncertain significance (May 26, 2024)
1-51976987-T-C		not specified	Uncertain significance (Aug 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAB3B	protein_coding	protein_coding	ENST00000371655	4	82809

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.315	0.670	125740	0	6	125746	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.945	104	135	0.771	0.00000803	1455
Missense in Polyphen		30	52.989	0.56615		582
Synonymous	0.807	45	52.4	0.858	0.00000318	423
Loss of Function	2.04	2	8.35	0.240	3.54e-7	98

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)	0.0000529	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Protein transport. Probably involved in vesicular traffic (By similarity). {ECO:0000250}.
• Pathway: Post-translational protein modification;Metabolism of proteins;RAB geranylgeranylation (Consensus)

Recessive Scores

• pRec: 0.175

Intolerance Scores

• loftool: 0.458
• rvis_EVS: -0.01
• rvis_percentile_EVS: 53.19

Haploinsufficiency Scores

• pHI: 0.610
• hipred: Y
• hipred_score: 0.624
• ghis: 0.534

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.668

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rab3b
• Phenotype: homeostasis/metabolism phenotype; growth/size/body region phenotype; 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; normal 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)

Zebrafish Information Network

• Gene name: rab3b
• Affected structure: yolk
• Phenotype tag: abnormal
• Phenotype quality: edematous

Gene ontology

• Biological process: intracellular protein transport;vesicle docking involved in exocytosis;protein secretion;regulation of exocytosis;peptidyl-cysteine methylation;antigen processing and presentation;Rab protein signal transduction;positive regulation of dopamine uptake involved in synaptic transmission;protein localization to plasma membrane;regulation of vesicle size;regulation of synaptic vesicle cycle
• Cellular component: cytoplasm;endosome;Golgi apparatus;cytosol;plasma membrane;synaptic vesicle;secretory granule;vesicle;perinuclear region of cytoplasm;extracellular exosome;dopaminergic synapse;anchored component of synaptic vesicle membrane
• Molecular function: GTPase activity;protein binding;GTP binding;GDP binding;GTP-dependent protein binding;myosin V binding