RAB2B

RAB2B, member RAS oncogene family, the group of RAB, member RAS oncogene GTPases

Basic information

Region (hg38): 14:21459020-21476960

Links

ENSG00000129472 ∙ NCBI:84932 ∙ OMIM:607466 ∙ HGNC:20246 ∙ Uniprot:Q8WUD1 ∙ 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 RAB2B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAB2B 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			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	0	0

Variants in RAB2B

This is a list of pathogenic ClinVar variants found in the RAB2B region.

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

Position	Type	Phenotype	Significance	ClinVar
14-21461227-C-T		not specified	Uncertain significance (Jun 30, 2023)
14-21461228-G-A		not specified	Uncertain significance (Sep 10, 2024)
14-21461237-G-A		not specified	Uncertain significance (Jan 27, 2022)
14-21461252-G-T		not specified	Uncertain significance (Jan 16, 2025)
14-21462369-A-G		not specified	Uncertain significance (Feb 28, 2025)
14-21462391-A-G		not specified	Uncertain significance (Jul 14, 2024)
14-21462396-T-C		not specified	Uncertain significance (Jan 07, 2025)
14-21463679-T-G		not specified	Uncertain significance (Mar 07, 2023)
14-21463694-T-G		not specified	Uncertain significance (Oct 01, 2024)
14-21463729-C-T		not specified	Uncertain significance (Jun 21, 2022)
14-21463754-G-A		not specified	Uncertain significance (Jan 16, 2025)
14-21468674-T-C		not specified	Uncertain significance (May 24, 2024)
14-21468680-C-T		not specified	Uncertain significance (Nov 07, 2022)
14-21468733-C-T		not specified	Uncertain significance (May 06, 2024)
14-21474914-T-C		not specified	Uncertain significance (Nov 15, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAB2B	protein_coding	protein_coding	ENST00000397762	8	17954

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00280	0.945	125733	0	14	125747	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.965	95	125	0.758	0.00000679	1411
Missense in Polyphen		19	40.213	0.47248		476
Synonymous	0.720	35	40.9	0.857	0.00000186	398
Loss of Function	1.69	6	12.4	0.482	5.26e-7	153

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000110	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000537	0.0000527
Middle Eastern	0.000110	0.000109
South Asian	0.0000655	0.0000653
Other	0.000332	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for protein transport from the endoplasmic reticulum to the Golgi complex. {ECO:0000305}.
• Pathway: Post-translational protein modification;Metabolism of proteins;RAB geranylgeranylation (Consensus)

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.642
• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.95

Haploinsufficiency Scores

• pHI: 0.380
• hipred: N
• hipred_score: 0.368
• ghis: 0.569

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.468

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rab2b

Gene ontology

• Biological process: intracellular protein transport;vesicle-mediated transport;Rab protein signal transduction;positive regulation of exocytosis
• Cellular component: Golgi membrane;endoplasmic reticulum membrane;plasma membrane;extracellular exosome;presynapse
• Molecular function: GTPase activity;protein binding;GTP binding