RGL3

ral guanine nucleotide dissociation stimulator like 3

Basic information

Region (hg38): 19:11384341-11419328

Links

ENSG00000205517 ∙ NCBI:57139 ∙ OMIM:616743 ∙ HGNC:30282 ∙ Uniprot:Q3MIN7 ∙ 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 RGL3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RGL3 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			68	5		73
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	68	6	0

Variants in RGL3

This is a list of pathogenic ClinVar variants found in the RGL3 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-11394430-C-T		not specified	Uncertain significance (May 23, 2023)
19-11394431-G-A		not specified	Uncertain significance (May 18, 2022)
19-11394446-G-C		not specified	Uncertain significance (Jun 16, 2024)
19-11394449-G-A		not specified	Uncertain significance (Jul 20, 2021)
19-11394464-T-C		not specified	Likely benign (Nov 22, 2021)
19-11394481-A-G		not specified	Uncertain significance (Nov 22, 2023)
19-11397252-C-T		not specified	Uncertain significance (Dec 06, 2022)
19-11397318-G-C		not specified	Uncertain significance (Jan 23, 2024)
19-11397331-C-T		not specified	Uncertain significance (May 30, 2022)
19-11397449-A-T		not specified	Uncertain significance (Sep 09, 2021)
19-11397489-C-T		not specified	Likely benign (Jun 22, 2021)
19-11397509-G-A		not specified	Uncertain significance (Jul 19, 2023)
19-11397521-G-A		not specified	Uncertain significance (Nov 03, 2023)
19-11397524-G-A		not specified	Likely benign (Dec 28, 2023)
19-11397558-C-T		not specified	Uncertain significance (Dec 03, 2021)
19-11397567-G-A		not specified	Uncertain significance (Sep 20, 2023)
19-11399874-G-A		not specified	Uncertain significance (Jan 06, 2023)
19-11399875-G-T		not specified	Uncertain significance (Dec 03, 2021)
19-11399889-G-A		not specified	Uncertain significance (May 17, 2023)
19-11399899-C-G		not specified	Uncertain significance (Feb 26, 2024)
19-11399922-G-A		not specified	Uncertain significance (Jul 14, 2021)
19-11399934-G-C		not specified	Uncertain significance (Apr 25, 2022)
19-11399964-C-T		not specified	Uncertain significance (May 31, 2023)
19-11400050-G-C		not specified	Uncertain significance (Dec 26, 2023)
19-11400064-C-G		not specified	Uncertain significance (Jun 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RGL3	protein_coding	protein_coding	ENST00000393423	19	35002

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.99e-32	0.0000134	125232	1	515	125748	0.00205

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.300	451	433	1.04	0.0000269	4526
Missense in Polyphen		158	147.39	1.072		1573
Synonymous	0.715	171	183	0.933	0.0000113	1512
Loss of Function	-0.347	46	43.5	1.06	0.00000271	414

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00363	0.00361
Ashkenazi Jewish	0.000307	0.000298
East Asian	0.00104	0.00103
Finnish	0.000242	0.000231
European (Non-Finnish)	0.00164	0.00158
Middle Eastern	0.00104	0.00103
South Asian	0.00757	0.00642
Other	0.00260	0.00228

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Guanine nucleotide exchange factor (GEF) for Ral-A. Potential effector of GTPase HRas and Ras-related protein M-Ras. Negatively regulates Elk-1-dependent gene induction downstream of HRas and MEKK1 (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.983
• rvis_EVS: -0.11
• rvis_percentile_EVS: 45.61

Haploinsufficiency Scores

• pHI: 0.0698
• hipred: N
• hipred_score: 0.241
• ghis: 0.530

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.107

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Rgl3

Gene ontology

• Biological process: small GTPase mediated signal transduction;positive regulation of GTPase activity
• Molecular function: Ral guanyl-nucleotide exchange factor activity