RAB4B

RAB4B, member RAS oncogene family, the group of RAB, member RAS oncogene GTPases

Basic information

Region (hg38): 19:40778215-40796942

Links

ENSG00000167578 ∙ NCBI:53916 ∙ OMIM:612945 ∙ HGNC:9782 ∙ Uniprot:P61018 ∙ 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 RAB4B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAB4B 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			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	0	0

Variants in RAB4B

This is a list of pathogenic ClinVar variants found in the RAB4B region.

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

Position	Type	Phenotype	Significance	ClinVar
19-40780072-C-G		not specified	Uncertain significance (Apr 07, 2023)
19-40780496-T-G		not specified	Uncertain significance (May 30, 2024)
19-40780497-T-G		not specified	Uncertain significance (May 30, 2024)
19-40783788-C-T		not specified	Uncertain significance (Feb 03, 2022)
19-40783792-G-A		not specified	Uncertain significance (Jan 23, 2024)
19-40783827-T-C		not specified	Uncertain significance (Apr 17, 2023)
19-40783830-G-A		not specified	Uncertain significance (Mar 30, 2022)
19-40783965-G-A		not specified	Uncertain significance (May 18, 2023)
19-40783997-C-G		not specified	Uncertain significance (Mar 26, 2024)
19-40784036-G-A		not specified	Uncertain significance (Dec 27, 2022)
19-40784050-G-C		not specified	Uncertain significance (Jan 26, 2023)
19-40784057-C-T		not specified	Uncertain significance (Jun 02, 2024)
19-40786733-C-T		not specified	Uncertain significance (Dec 28, 2023)
19-40786892-G-C		not specified	Uncertain significance (Mar 20, 2023)
19-40786904-C-T		not specified	Uncertain significance (Jan 17, 2024)
19-40786905-G-A		not specified	Uncertain significance (Jan 23, 2023)
19-40786937-G-A		not specified	Uncertain significance (Nov 07, 2023)
19-40786948-G-T		not specified	Uncertain significance (Nov 09, 2021)
19-40786950-C-T		not specified	Uncertain significance (Jun 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAB4B	protein_coding	protein_coding	ENST00000594800	7	18727

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.671	0.328	125732	0	16	125748	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.924	111	142	0.782	0.00000975	1369
Missense in Polyphen		34	51.415	0.66128		493
Synonymous	0.872	51	59.6	0.856	0.00000413	437
Loss of Function	2.72	2	12.3	0.163	5.98e-7	140

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000972	0.0000967
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.302
• rvis_EVS: -0.54
• rvis_percentile_EVS: 20.26

Haploinsufficiency Scores

• pHI: 0.373
• hipred: N
• hipred_score: 0.314
• ghis: 0.597

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.837

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rab4b

Gene ontology

• Biological process: intracellular protein transport;regulation of endocytosis;Rab protein signal transduction;neutrophil degranulation;glucose import
• Cellular component: endosome;plasma membrane;secretory granule membrane;insulin-responsive compartment;perinuclear region of cytoplasm;recycling endosome
• Molecular function: molecular_function;GTPase activity;protein binding;GTP binding