RAB3D

RAB3D, member RAS oncogene family, the group of RAB, member RAS oncogene GTPases

Basic information

Region (hg38): 19:11322068-11346270

Previous symbols: [ "GOV" ]

Links

ENSG00000105514 ∙ NCBI:9545 ∙ OMIM:604350 ∙ HGNC:9779 ∙ Uniprot:O95716 ∙ 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 RAB3D gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAB3D 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				1		1
missense			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	12	1	0

Variants in RAB3D

This is a list of pathogenic ClinVar variants found in the RAB3D region.

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

Position	Type	Phenotype	Significance	ClinVar
19-11325497-C-T		not specified	Uncertain significance (Mar 06, 2023)
19-11325526-G-A		not specified	Uncertain significance (Apr 07, 2023)
19-11325529-C-T		not specified	Uncertain significance (Mar 31, 2024)
19-11325580-C-G		not specified	Uncertain significance (Nov 13, 2024)
19-11335453-C-T		not specified	Uncertain significance (May 18, 2023)
19-11335482-G-T		not specified	Uncertain significance (Dec 21, 2022)
19-11335491-C-T		not specified	Uncertain significance (Aug 20, 2024)
19-11335495-C-T		not specified	Uncertain significance (Dec 08, 2023)
19-11335566-G-A		not specified	Uncertain significance (Jan 23, 2024)
19-11335657-G-T			Benign (Jun 26, 2018)
19-11335735-G-A		not specified	Uncertain significance (May 01, 2024)
19-11335758-C-T		not specified	Uncertain significance (Aug 26, 2022)
19-11335759-G-A		not specified	Uncertain significance (Jan 31, 2024)
19-11337179-T-C		not specified	Uncertain significance (Mar 14, 2023)
19-11337228-C-T		not specified	Uncertain significance (Dec 11, 2023)
19-11337257-G-A		not specified	Uncertain significance (May 14, 2024)
19-11337268-G-A			Likely benign (Jan 01, 2023)
19-11337272-G-A		not specified	Uncertain significance (Oct 12, 2024)
19-11337273-C-T		not specified	Uncertain significance (Aug 19, 2024)
19-11337278-C-T		not specified	Uncertain significance (Aug 15, 2023)
19-11337346-G-C		not specified	Uncertain significance (Oct 24, 2024)
19-11337366-G-A		not specified	Uncertain significance (Jun 24, 2022)
19-11342861-T-C		not specified	Uncertain significance (Oct 25, 2024)
19-11342864-C-T		not specified	Uncertain significance (May 10, 2024)
19-11342870-A-T		not specified	Uncertain significance (Sep 06, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAB3D	protein_coding	protein_coding	ENST00000222120	4	24225

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000133	0.405	125721	0	27	125748	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.892	113	143	0.790	0.00000961	1444
Missense in Polyphen		43	54.191	0.79349		595
Synonymous	0.0998	61	62.0	0.984	0.00000483	427
Loss of Function	0.373	8	9.22	0.868	4.82e-7	94

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000293	0.000293
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000967	0.0000967
Middle Eastern	0.000163	0.000163
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Protein transport. Probably involved in regulated exocytosis (By similarity). {ECO:0000250}.
• Pathway: Pancreatic secretion - Homo sapiens (human);Neutrophil degranulation;Post-translational protein modification;Metabolism of proteins;Innate Immune System;Immune System;RAB geranylgeranylation (Consensus)

Recessive Scores

• pRec: 0.215

Intolerance Scores

• loftool: 0.449
• rvis_EVS: 0.11
• rvis_percentile_EVS: 61.73

Haploinsufficiency Scores

• pHI: 0.130
• hipred: N
• hipred_score: 0.335
• ghis: 0.522

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.932

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rab3d
• 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system 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); growth/size/body region phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: intracellular protein transport;vesicle docking involved in exocytosis;protein secretion;regulation of exocytosis;peptidyl-cysteine methylation;Rab protein signal transduction;neutrophil degranulation;bone resorption;protein localization to plasma membrane;positive regulation of regulated secretory pathway
• Cellular component: endosome;cytoplasmic microtubule;plasma membrane;synaptic vesicle;vesicle;azurophil granule membrane;zymogen granule;extracellular exosome;secretory vesicle
• Molecular function: GTPase activity;GTP binding;GTP-dependent protein binding;myosin V binding