RAB5B

RAB5B, member RAS oncogene family, the group of RAB, member RAS oncogene GTPases

Basic information

Region (hg38): 12:55973913-55996683

Links

ENSG00000111540 ∙ NCBI:5869 ∙ OMIM:179514 ∙ HGNC:9784 ∙ Uniprot:P61020 ∙ 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 RAB5B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAB5B 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			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	1	0

Variants in RAB5B

This is a list of pathogenic ClinVar variants found in the RAB5B region.

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

Position	Type	Phenotype	Significance	ClinVar
12-55986989-A-G		not specified	Uncertain significance (Apr 05, 2023)
12-55987006-A-G		not specified	Uncertain significance (Aug 11, 2022)
12-55990066-G-A		not specified	Uncertain significance (Jun 12, 2023)
12-55990739-A-G		not specified	Uncertain significance (May 06, 2024)
12-55990772-G-C		RAB5B-associated surfactant dysfunction disorder	Uncertain significance (Jan 10, 2019)
12-55991369-G-C		not specified	Uncertain significance (Oct 19, 2021)
12-55992121-C-T		not specified	Uncertain significance (Dec 13, 2022)
12-55992126-A-G		not specified	Uncertain significance (Aug 02, 2021)
12-55992170-T-C			Likely benign (Jun 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAB5B	protein_coding	protein_coding	ENST00000360299	5	20794

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0264	0.963	125743	0	5	125748	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.32	82	123	0.666	0.00000663	1412
Missense in Polyphen		21	48.21	0.4356		556
Synonymous	-0.413	50	46.4	1.08	0.00000242	410
Loss of Function	2.23	5	14.0	0.358	9.34e-7	130

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000265	0.0000264
Middle Eastern	0.000109	0.000109
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: Endocytosis - Homo sapiens (human);Phagosome - Homo sapiens (human);Vasopressin-regulated water reabsorption - Homo sapiens (human);Amoebiasis - Homo sapiens (human);Tuberculosis - Homo sapiens (human);Ras signaling pathway - Homo sapiens (human);Ras Signaling;Neutrophil degranulation;Vesicle-mediated transport;TBC/RABGAPs;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Innate Immune System;Immune System;Clathrin-mediated endocytosis;Rab regulation of trafficking;RAB GEFs exchange GTP for GDP on RABs;RAB geranylgeranylation (Consensus)

Recessive Scores

• pRec: 0.125

Intolerance Scores

• loftool: 0.336
• rvis_EVS: -0.12
• rvis_percentile_EVS: 44.54

Haploinsufficiency Scores

• pHI: 0.720
• hipred: Y
• hipred_score: 0.685
• ghis: 0.570

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.999

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rab5b

Zebrafish Information Network

• Gene name: rab5b
• Affected structure: skeletal muscle
• Phenotype tag: abnormal
• Phenotype quality: morphology

Gene ontology

• Biological process: intracellular protein transport;endocytosis;endosome organization;antigen processing and presentation;regulation of endocytosis;Rab protein signal transduction;neutrophil degranulation;plasma membrane to endosome transport
• Cellular component: endosome;early endosome;plasma membrane;membrane;endocytic vesicle;secretory granule membrane;early endosome membrane;melanosome;intracellular membrane-bounded organelle;extracellular exosome;anchored component of synaptic vesicle membrane
• Molecular function: GTPase activity;protein binding;GTP binding;GDP binding;GTP-dependent protein binding