RAB3C

RAB3C, member RAS oncogene family, the group of RAB, member RAS oncogene GTPases

Basic information

Region (hg38): 5:58582221-58859394

Links

ENSG00000152932 ∙ NCBI:115827 ∙ OMIM:612829 ∙ HGNC:30269 ∙ Uniprot:Q96E17 ∙ 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 RAB3C gene.

• not_specified (25 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAB3C gene is commonly pathogenic or not. These statistics are base on transcript: NM_000138453.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			26			26
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	26	0	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAB3C	protein_coding	protein_coding	ENST00000282878	5	277166

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		125699	0	9	125708	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.26	88	128	0.688	0.00000683	1521
Missense in Polyphen		12	35.857	0.33466		407
Synonymous	0.277	43	45.4	0.948	0.00000257	404
Loss of Function	1.16	7	11.2	0.625	5.57e-7	131

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000204	0.000198
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000622	0.0000616
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: 0.142

Intolerance Scores

• loftool: 0.504
• rvis_EVS: -0.3
• rvis_percentile_EVS: 32.62

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.903

Gene Damage Prediction

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

Gene ontology

• Biological process: intracellular protein transport;vesicle docking involved in exocytosis;protein secretion;regulation of exocytosis;antigen processing and presentation;Rab protein signal transduction;protein localization to plasma membrane
• Cellular component: endosome;cytosol;plasma membrane;synaptic vesicle;vesicle;perinuclear region of cytoplasm;anchored component of synaptic vesicle membrane
• Molecular function: GTPase activity;protein binding;GTP binding;GTP-dependent protein binding;myosin V binding