RAB2A

RAB2A, member RAS oncogene family, the group of RAB, member RAS oncogene GTPases

Basic information

Region (hg38): 8:60516936-60623644

Previous symbols: [ "RAB2" ]

Links

ENSG00000104388 ∙ NCBI:5862 ∙ OMIM:179509 ∙ HGNC:9763 ∙ Uniprot:P61019 ∙ 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 RAB2A gene.

• not_specified (5 variants)
• not_provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAB2A gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002865.3. 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				1		1
missense			5			5
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)				1		1
Total	0	0	5	2	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAB2A	protein_coding	protein_coding	ENST00000262646	8	106771

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.989	0.0109	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.99	24	114	0.211	0.00000599	1385
Missense in Polyphen		2	39.665	0.050422		477
Synonymous	0.856	31	37.7	0.823	0.00000207	372
Loss of Function	3.42	0	13.6	0.00	7.39e-7	160

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for protein transport from the endoplasmic reticulum to the Golgi complex.
• Pathway: AMPK signaling pathway - Homo sapiens (human);Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;Post-translational protein modification;Metabolism of proteins;Golgi Cisternae Pericentriolar Stack Reorganization;Mitotic Prophase;M Phase;Cell Cycle;RAB geranylgeranylation;Cell Cycle, Mitotic (Consensus)

Recessive Scores

• pRec: 0.240

Intolerance Scores

• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.63

Haploinsufficiency Scores

• pHI: 0.660
• hipred: Y
• hipred_score: 0.825
• ghis: 0.680

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.914

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rab2a

Gene ontology

• Biological process: intracellular protein transport;endoplasmic reticulum to Golgi vesicle-mediated transport;Golgi organization;Rab protein signal transduction;post-translational protein modification
• Cellular component: Golgi membrane;nucleus;lysosomal membrane;endoplasmic reticulum membrane;Golgi apparatus;cytosol;endoplasmic reticulum-Golgi intermediate compartment membrane;melanosome;extracellular exosome
• Molecular function: GTPase activity;protein binding;GTP binding;GDP binding