RABEP1

protein-coding

rabaptin, RAB GTPase binding effector protein 1

Gene summary

Enables protein domain specific binding activity and protein homodimerization activity. Involved in vesicle-mediated transport. Located in cytosol; endocytic vesicle; and endosome. Part of protein-containing complex. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_004703.6

Inheritance

—

ClinVar variants

U:85B:6

Top phenotype

Teratoma

gnomAD constraint

pLI —, LoF o/e 0.15

Max pathogenic AF

—

Genomic locus

chr17:5,282,265-5,386,340

External References & Databases

Ensembl (ENSG00000029725)

Transcript & Mutation Effects

hg38 • Region Span ~104.1 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 RABEP1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 79

not providedTotal: 5

TeratomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_004703.6. 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			2 clinvar	4 clinvar		6
missense			80 clinvar	2 clinvar		82
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	85	6	0	91

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 78 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_004703.6	RefSeq	NP_004694.2	18	MANE Select
ENST00000537505.6	Ensembl	ENSP00000445408.2	18	MANE Select
NM_001083585.3	RefSeq	NP_001077054.1	17	Standard
NM_001291581.2	RefSeq	NP_001278510.1	17	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
rabep1	Danio rerio	Structure: post-vent region Quality: curved ventral abnormal

Gene / Model

Organism

Observed Phenotype

rabep1

Danio rerio

Structure: post-vent region

Quality: curved ventral

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Endocytosis - Homo sapiens (human)
Vesicle-mediated transport
TBC/RABGAPs
Membrane Trafficking
Rab regulation of trafficking

Biological Process

Golgi to plasma membrane transport
endocytosis
apoptotic process
regulation of signaling receptor activity
protein transport

Molecular Function

GTPase activator activity
protein binding
growth factor activity
protein domain specific binding
protein homodimerization activity

Cellular Component

endosome
early endosome
endocytic vesicle
early endosome membrane
protein-containing complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000262477
Coding exons: 18
Length: 103572
Individuals with no LoFs: 124776
Homozygous LoFs: 0
Heterozygous LoFs: 16
Defined: 124792
p: 0.0000641

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.86	330	439	0.751	0.0000233	5655
Missense (PolyPhen)		109	183.47	0.59412		2319
Synonymous	0.491	154	162	0.951	0.00000854	1534
Loss of Function	5.82	8	54.2	0.148	0.00000272	656

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00017	0.00017	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000027	0.000026	rare
South Asian	0.00023	0.00023	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Rab effector protein acting as linker between gamma- adaptin, RAB4A and RAB5A. Involved in endocytic membrane fusion and membrane trafficking of recycling endosomes. Involved in KCNH1 channels trafficking to and from the cell membrane (PubMed:22841712). Stimulates RABGEF1 mediated nucleotide exchange on RAB5A. {ECO:0000269|PubMed:10698684, ECO:0000269|PubMed:11452015, ECO:0000269|PubMed:12773381, ECO:0000269|PubMed:22841712, ECO:0000269|PubMed:8521472}.;

Recessive Scores

pRec: 0.165

Intolerance Scores

RVIS EVS: -1.2
RVIS percentile EVS: 5.83

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.837

Gene Damage Prediction

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