RABGGTA

protein-coding

Rab geranylgeranyltransferase subunit alpha, the group of Prenyltransferase alpha subunit repeat containing

Gene summary

Predicted to enable small GTPase binding activity. Predicted to contribute to Rab geranylgeranyltransferase activity. Predicted to be involved in endoplasmic reticulum to Golgi vesicle-mediated transport and protein geranylgeranylation. Predicted to be located in cytosol and plasma membrane. Predicted to be part of Rab-protein geranylgeranyltransferase complex. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_182836.3

Inheritance

—

ClinVar variants

U:103B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.57

Max pathogenic AF

—

Genomic locus

chr14:24,265,538-24,271,611

External References & Databases

Ensembl (ENSG00000100949)

Transcript & Mutation Effects

hg38 • Region Span ~6.1 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 RABGGTA variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 95

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_182836.3. 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	2
missense			99 clinvar	1 clinvar		100
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	103	1	1	105

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 34 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_182836.3	RefSeq	NP_878256.1	16	MANE Select
ENST00000216840.11	Ensembl	ENSP00000216840.6	16	MANE Select
NM_004581.5	RefSeq	NP_004572.3	16	Standard
ENST00000399409.7	Ensembl	ENSP00000382341.3	16	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

TP53 Regulates Transcription of Cell Death Genes
Gene expression (Transcription)
Generic Transcription Pathway
Post-translational protein modification
Metabolism of proteins

Biological Process

cellular protein modification process
visual perception
protein geranylgeranylation
regulation of apoptotic process
post-translational protein modification

Molecular Function

Rab geranylgeranyltransferase activity
zinc ion binding
Rab GTPase binding
protein heterodimerization activity

Cellular Component

nucleoplasm
cytoplasm
cytosol
plasma membrane
Rab-protein geranylgeranyltransferase complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000399409
Coding exons: 16
Length: 6202
Individuals with no LoFs: 124624
Homozygous LoFs: 0
Heterozygous LoFs: 51
Defined: 124675
p: 0.000205

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.530	307	334	0.918	0.0000207	3583
Missense (PolyPhen)		93	110.06	0.84496		1200
Synonymous	0.679	129	139	0.927	0.00000778	1179
Loss of Function	2.47	22	38.5	0.571	0.00000241	363

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00020	0.00020	rare
Ashkenazi Jewish	0.00040	0.00040	rare
East Asian	0.00030	0.00028	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00017	0.00017	rare
South Asian	0.00041	0.00039	rare
Other	0.00050	0.00050	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Catalyzes the transfer of a geranylgeranyl moiety from geranylgeranyl diphosphate to both cysteines of Rab proteins with the C-terminal sequence -XXCC, -XCXC and -CCXX, such as RAB1A, RAB3A, RAB5A and RAB7A. {ECO:0000269|PubMed:7991565}.;

Recessive Scores

pRec: 0.135

Intolerance Scores

RVIS EVS: -0.75
RVIS percentile EVS: 13.67

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): H
Indispensability pred.: E
Indispensability score: 0.656

Gene Damage Prediction

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