RABEP2

protein-coding

rabaptin, RAB GTPase binding effector protein 2

Gene summary

Predicted to enable GTPase activator activity and growth factor activity. Involved in regulation of cilium assembly. Located in centrosome; ciliary basal body; and cytosol. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_024816.3

Inheritance

—

ClinVar variants

U:106B:5

Top phenotype

Myoepithelial tumor

gnomAD constraint

pLI —, LoF o/e 0.34

Max pathogenic AF

—

Genomic locus

chr16:28,904,421-28,936,526

External References & Databases

Ensembl (ENSG00000177548)

Transcript & Mutation Effects

hg38 • Region Span ~32.1 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 RABEP2 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 93

not providedTotal: 3

Myoepithelial tumorTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024816.3. 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	1 clinvar	3
missense			97 clinvar	3 clinvar		100
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			7 clinvar			7
Total	0	0	106	4	1	111

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 43 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024816.3	RefSeq	NP_079092.2	13	MANE Select
ENST00000358201.9	Ensembl	ENSP00000350934.4	13	MANE Select
ENST00000357573.10	Ensembl	ENSP00000350186.6	11	Standard
ENST00000357573.11	Ensembl	ENSP00000350186.6	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

endocytosis
regulation of signaling receptor activity
protein transport
positive regulation of GTPase activity

Molecular Function

GTPase activator activity
growth factor activity

Cellular Component

early endosome
cytosol
intracellular membrane-bounded organelle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000358201
Coding exons: 13
Length: 32106
Individuals with no LoFs: 124731
Homozygous LoFs: 0
Heterozygous LoFs: 74
Defined: 124805
p: 0.000297

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.432	337	360	0.936	0.0000243	3599
Missense (PolyPhen)		65	73.254	0.88732		740
Synonymous	0.626	156	166	0.938	0.0000109	1198
Loss of Function	3.43	11	31.9	0.344	0.00000162	334

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00039	0.00039	rare
Latino/Admixed American	0.00029	0.00029	rare
Ashkenazi Jewish	0.0040	0.0037	notable
East Asian	0.000056	0.000056	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00016	0.00015	rare
South Asian	0.000066	0.000065	rare
Other	0.00019	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Plays a role in membrane trafficking and in homotypic early endosome fusion. {ECO:0000269|PubMed:9524116}.;

Recessive Scores

pRec: 0.239

Intolerance Scores

LoFtool: 0.502
RVIS EVS: -0.69
RVIS percentile EVS: 15.12

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.104

Gene Damage Prediction

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