RAB42

protein-coding

RAB42, member RAS oncogene family, the group of RAB, member RAS oncogene GTPases

Gene summary

Predicted to enable GTPase activity. Predicted to be involved in small GTPase-mediated signal transduction. Predicted to be located in membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001193532.3

Inheritance

—

ClinVar variants

U:29B:2

Top phenotype

Autism

gnomAD constraint

pLI —, LoF o/e 1.64

Max pathogenic AF

—

Genomic locus

chr1:28,592,200-28,595,449

External References & Databases

Ensembl (ENSG00000188060)

Transcript & Mutation Effects

hg38 • Region Span ~3.2 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 RAB42 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 30

AutismTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001193532.3. 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
missense			29 clinvar	1 clinvar		30
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	29	2	0	31

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 8 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001193532.3	RefSeq	NP_001180461.1	2	MANE Select
ENST00000465518.3	Ensembl	ENSP00000491546.1	2	MANE Select
NM_001385188.1	RefSeq	NP_001372117.1	2	Standard
NM_152304.3	RefSeq	NP_689517.1	1	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

Molecular Function

GTPase activity
GTP binding

Cellular Component

membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000373826
Coding exons: 1
Length: 3244
Individuals with no LoFs: 125684
Homozygous LoFs: 0
Heterozygous LoFs: 11
Defined: 125695
p: 0.0000438

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.108	62	59.6	1.04	0.00000327	673
Missense (PolyPhen)		23	20.136	1.1422		223
Synonymous	0.766	22	27.1	0.813	0.00000156	214
Loss of Function	-0.797	3	1.83	1.64	7.81e-8	20

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00018	0.00018	rare
Latino/Admixed American	0.000061	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000027	0.000026	rare
South Asian	0.000098	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.708
RVIS EVS: 0.72
RVIS percentile EVS: 85.92

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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