RAB20

protein-coding

RAB20, member RAS oncogene family, the group of RAB, member RAS oncogene GTPases

Gene summary

Predicted to enable GTPase activity. Involved in phagosome acidification and phagosome-lysosome fusion. Located in Golgi apparatus and phagocytic vesicle. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_017817.3

Inheritance

—

ClinVar variants

U:38B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.73

Max pathogenic AF

—

Genomic locus

chr13:110,523,066-110,561,722

External References & Databases

Ensembl (ENSG00000139832)

Transcript & Mutation Effects

hg38 • Region Span ~38.7 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 RAB20 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 39

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_017817.3. 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						0
missense			38 clinvar	1 clinvar		39
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	38	1	0	39

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 9 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_017817.3	RefSeq	NP_060287.1	2	MANE Select
ENST00000267328.5	Ensembl	ENSP00000267328.3	2	MANE Select
ENST00000907762.1	Ensembl	ENSP00000577821.1	2	Standard
ENST00000907762.2	Ensembl	ENSP00000577821.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Post-translational protein modification
Metabolism of proteins
RAB geranylgeranylation

Biological Process

intracellular protein transport
endocytosis
regulation of endocytosis
Rab protein signal transduction
cellular response to interferon-gamma

Molecular Function

GTPase activity
GTP binding

Cellular Component

endosome
early endosome
Golgi apparatus
plasma membrane
endocytic vesicle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000267328
Coding exons: 2
Length: 38664
Individuals with no LoFs: 125739
Homozygous LoFs: 0
Heterozygous LoFs: 6
Defined: 125745
p: 0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.697	118	141	0.835	0.00000788	1529
Missense (PolyPhen)		51	72.597	0.70251		772
Synonymous	0.431	58	62.3	0.931	0.00000383	465
Loss of Function	0.580	4	5.46	0.732	2.31e-7	72

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)	0.000046	0.000044	rare
South Asian	0	0.0	absent
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Plays a role in apical endocytosis/recycling. Plays a role in the maturation and acidification of phagosomes that engulf pathogens, such as S.aureus and M.tuberculosis. Plays a role in the fusion of phagosomes with lysosomes. {ECO:0000269|PubMed:21255211}.;

Recessive Scores

pRec: 0.131

Intolerance Scores

RVIS EVS: -0.16
RVIS percentile EVS: 41.64

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.101

Gene Damage Prediction

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