RABGGTB

Rab geranylgeranyltransferase subunit beta, the group of Small nucleolar RNA protein coding host genes

Basic information

Region (hg38): 1:75786197-75795086

Links

ENSG00000137955 ∙ NCBI:5876 ∙ OMIM:179080 ∙ HGNC:9796 ∙ Uniprot:P53611 ∙ 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 RABGGTB gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RABGGTB 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			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	1	0

Variants in RABGGTB

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

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

Position	Type	Phenotype	Significance	ClinVar
1-75787507-A-G		not specified	Uncertain significance (Feb 02, 2024)
1-75787572-A-G		not specified	Uncertain significance (Aug 17, 2022)
1-75789290-A-C		not specified	Uncertain significance (Feb 06, 2023)
1-75789959-C-T		not specified	Uncertain significance (May 17, 2023)
1-75789975-T-G		not specified	Uncertain significance (Jun 29, 2023)
1-75790051-A-G		not specified	Uncertain significance (Aug 02, 2023)
1-75792183-C-G		not specified	Uncertain significance (Mar 28, 2024)
1-75792279-A-G			Likely benign (Jan 01, 2024)
1-75792299-C-T		not specified	Uncertain significance (Jan 10, 2022)
1-75794151-T-C		not specified	Uncertain significance (Dec 19, 2022)
1-75794162-A-G		not specified	Uncertain significance (Dec 17, 2023)
1-75794511-T-C		not specified	Uncertain significance (Feb 13, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RABGGTB	protein_coding	protein_coding	ENST00000319942	9	8886

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00787	0.989	125723	0	23	125746	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.48	125	181	0.690	0.00000895	2176
Missense in Polyphen		36	71.455	0.50381		872
Synonymous	0.0221	65	65.2	0.997	0.00000363	611
Loss of Function	2.62	7	19.5	0.359	9.21e-7	241

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000177	0.000177
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.000123	0.000114
Middle Eastern	0.000272	0.000272
South Asian	0.00	0.00
Other	0.00	0.00

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.
• Pathway: 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: 0.124

Intolerance Scores

• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.42

Haploinsufficiency Scores

• pHI: 0.607
• hipred: Y
• hipred_score: 0.749
• ghis: 0.648

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.964

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rabggtb

Zebrafish Information Network

• Gene name: rabggtb
• Affected structure: muscle
• Phenotype tag: abnormal
• Phenotype quality: damaged

Gene ontology

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