RAB2A

protein-coding

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

Gene summary

The protein encoded by this gene belongs to the Rab family, members of which are small molecular weight guanosine triphosphatases (GTPases) that contain highly conserved domains involved in GTP binding and hydrolysis. The Rabs are membrane-bound proteins, involved in vesicular fusion and trafficking. This protein is a resident of pre-Golgi intermediates, and is required for protein transport from the endoplasmic reticulum (ER) to the Golgi complex. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]

Previous symbols:

RAB2

MANE transcript

NM_002865.3

Inheritance

—

ClinVar variants

U:8B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr8:60,516,936-60,623,644

External References & Databases

Ensembl (ENSG00000104388)

Transcript & Mutation Effects

hg38 • Region Span ~106.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to RAB2A variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 5

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002865.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	1 clinvar		2
missense			5 clinvar			5
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	8	1	0	9

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 33 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_002865.3	RefSeq	NP_002856.1	8	MANE Select
ENST00000262646.12	Ensembl	ENSP00000262646.7	8	MANE Select
NM_001242644.1	RefSeq	NP_001229573.1	7	Standard
ENST00000452437.1	Ensembl	ENSP00000398054.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

Biological Process

intracellular protein transport
endoplasmic reticulum to Golgi vesicle-mediated transport
Golgi organization
Rab protein signal transduction
post-translational protein modification

Molecular Function

GTPase activity
protein binding
GTP binding
GDP binding

Cellular Component

Golgi membrane
nucleus
lysosomal membrane
endoplasmic reticulum membrane
Golgi apparatus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000262646
Coding exons: 8
Length: 106771
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.99	24	114	0.211	0.00000599	1385
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Required for protein transport from the endoplasmic reticulum to the Golgi complex.;

Recessive Scores

pRec: 0.240

Intolerance Scores

RVIS EVS: 0.01
RVIS percentile EVS: 54.63

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.914

Gene Damage Prediction

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