RABGGTA

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

Basic information

Region (hg38): 14:24265538-24271611

Links

ENSG00000100949 ∙ NCBI:5875 ∙ OMIM:601905 ∙ HGNC:9795 ∙ Uniprot:Q92696 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RABGGTA gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RABGGTA gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			46			46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	46	0	1

Variants in RABGGTA

This is a list of pathogenic ClinVar variants found in the RABGGTA region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
14-24265662-C-T		not specified	Uncertain significance (Jan 31, 2024)
14-24265710-G-A		not specified	Uncertain significance (Dec 14, 2021)
14-24265710-G-C		not specified	Uncertain significance (Oct 06, 2024)
14-24265752-G-A		not specified	Uncertain significance (Nov 29, 2023)
14-24265753-C-G		not specified	Uncertain significance (Dec 10, 2024)
14-24266459-C-T		not specified	Uncertain significance (Mar 02, 2023)
14-24266460-G-A		not specified	Uncertain significance (Apr 09, 2024)
14-24266478-C-T		not specified	Uncertain significance (Oct 09, 2024)
14-24266786-C-T		not specified	Uncertain significance (Dec 15, 2023)
14-24266825-T-C		not specified	Uncertain significance (May 27, 2022)
14-24267683-G-A		not specified	Uncertain significance (Oct 30, 2024)
14-24267689-C-T		not specified	Uncertain significance (Dec 20, 2024)
14-24267701-T-A		not specified	Uncertain significance (May 06, 2022)
14-24267710-C-T		not specified	Uncertain significance (Jan 10, 2022)
14-24267723-C-G		not specified	Uncertain significance (Jul 12, 2023)
14-24267736-C-T		not specified	Uncertain significance (Feb 13, 2025)
14-24267760-C-T		not specified	Uncertain significance (Jan 23, 2023)
14-24267773-C-T		not specified	Uncertain significance (Nov 10, 2022)
14-24267893-G-C		not specified	Uncertain significance (Jan 18, 2025)
14-24267905-C-T		not specified	Uncertain significance (Jan 09, 2024)
14-24268150-T-A		not specified	Uncertain significance (May 13, 2024)
14-24268390-G-A		not specified	Uncertain significance (Jun 02, 2023)
14-24268399-C-T		not specified	Uncertain significance (Jul 20, 2021)
14-24268412-C-T		not specified	Uncertain significance (Feb 07, 2025)
14-24268417-C-A		not specified	Uncertain significance (Sep 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RABGGTA	protein_coding	protein_coding	ENST00000399409	16	6202

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.75e-10	0.990	124624	0	51	124675	0.000205

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.530	307	334	0.918	0.0000207	3583
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000203	0.000203
Ashkenazi Jewish	0.000398	0.000398
East Asian	0.000304	0.000278
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.000170	0.000168
Middle Eastern	0.000304	0.000278
South Asian	0.000409	0.000392
Other	0.000497	0.000495

dbNSFP

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}.
• Pathway: TP53 Regulates Transcription of Cell Death Genes;Gene expression (Transcription);Generic Transcription Pathway;Post-translational protein modification;Metabolism of proteins;TP53 Regulates Transcription of Cell Death Genes;RNA Polymerase II Transcription;TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain;Transcriptional Regulation by TP53;RAB geranylgeranylation;Signaling events mediated by PRL (Consensus)

Recessive Scores

• pRec: 0.135

Intolerance Scores

• rvis_EVS: -0.75
• rvis_percentile_EVS: 13.67

Haploinsufficiency Scores

• pHI: 0.309
• hipred: N
• hipred_score: 0.372
• ghis: 0.552

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.656

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rabggta
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); immune system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; hematopoietic system phenotype; pigmentation phenotype

Gene ontology

• Biological process: cellular protein modification process;visual perception;protein geranylgeranylation;regulation of apoptotic process;post-translational protein modification;protein-containing complex assembly
• Cellular component: nucleoplasm;cytoplasm;cytosol;plasma membrane;Rab-protein geranylgeranyltransferase complex
• Molecular function: Rab geranylgeranyltransferase activity;zinc ion binding;Rab GTPase binding;protein heterodimerization activity