RABL3

protein-coding

RAB, member of RAS oncogene family like 3, the group of RAB like GTPases

Gene summary

Enables G protein activity. Involved in positive regulation of cilium assembly; regulation of Ras protein signal transduction; and regulation of protein lipidation. Predicted to be located in Golgi apparatus and centrosome. Predicted to be active in endomembrane system. Implicated in pancreatic cancer. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_173825.5

Inheritance

ClinVar variants

U:34B:8

Top phenotype

Pancreatic cancer, susceptibility to, 5

gnomAD constraint

pLI —, LoF o/e 0.52

Max pathogenic AF

—

Genomic locus

chr3:120,684,938-120,742,993

External References & Databases

Ensembl (ENSG00000144840)

Transcript & Mutation Effects

hg38 • Region Span ~58.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

pancreatic cancer, susceptibility to, 5LIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0032867

Submitter: Genomics England PanelApp

familial pancreatic carcinomaSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0015278

Submitter: Orphanet

Clinical Genomic Database (CGD)

Pancreatic cancer, susceptibility to, 5AD

Manifestation: Oncologic

Intervention: Oncologic

Rationale: Individuals are reported to be at increased risk of pancreatic cancer (as well as other neoplasms), and awareness may allow early diagnosis and management

Refs: 31406347

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to RABL3 variants in ClinVar

5 Conditions Cataloged

not specifiedTotal: 17

RABL3-related disorderTotal: 16

not providedTotal: 3

Familial adenomatous polyposis 2Total: 1

Pancreatic cancer, susceptibility to, 5Total: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_173825.5. 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	6 clinvar		8
missense			26 clinvar	2 clinvar		28
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	34	8	0	42

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 23 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_173825.5	RefSeq	NP_776186.2	8	MANE Select
ENST00000273375.8	Ensembl	ENSP00000273375.4	8	MANE Select
NM_001363964.1	RefSeq	NP_001350893.1	7	Standard
NM_001363965.1	RefSeq	NP_001350894.1	9	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

intracellular protein transport
Rab protein signal transduction

Molecular Function

GTPase activity
GTP binding

Cellular Component

cell

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000273375
Coding exons: 8
Length: 56313
Individuals with no LoFs: 125731
Homozygous LoFs: 0
Heterozygous LoFs: 17
Defined: 125748
p: 0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.432	115	129	0.893	0.00000675	1530
Missense (PolyPhen)		35	44.737	0.78236		535
Synonymous	-0.134	48	46.8	1.02	0.00000237	448
Loss of Function	1.65	7	13.5	0.517	5.70e-7	177

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00011	0.00011	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.109

Intolerance Scores

LoFtool: 0.511
RVIS EVS: -0.21
RVIS percentile EVS: 38.58

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.925

Gene Damage Prediction

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