RGL2

ral guanine nucleotide dissociation stimulator like 2

Basic information

Region (hg38): 6:33291654-33298942

Previous symbols: [ "RAB2L" ]

Links

ENSG00000237441 ∙ NCBI:5863 ∙ OMIM:602306 ∙ HGNC:9769 ∙ Uniprot:O15211 ∙ 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 RGL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RGL2 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	2
missense			41	6	1	48
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	42	7	2

Variants in RGL2

This is a list of pathogenic ClinVar variants found in the RGL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-33292157-C-A		not specified	Uncertain significance (May 23, 2023)
6-33292157-C-T		not specified	Uncertain significance (Nov 07, 2022)
6-33292305-T-G		not specified	Uncertain significance (Jun 10, 2024)
6-33292463-A-G		not specified	Uncertain significance (May 02, 2024)
6-33292487-G-A		not specified	Uncertain significance (May 13, 2024)
6-33292504-A-G		not specified	Uncertain significance (Dec 21, 2023)
6-33292507-C-T		not specified	Uncertain significance (Oct 20, 2023)
6-33293041-T-C		not specified	Uncertain significance (Jan 20, 2023)
6-33293126-C-T		not specified	Likely benign (Nov 16, 2021)
6-33293143-C-A		not specified	Uncertain significance (Jan 08, 2024)
6-33293189-G-C		not specified	Uncertain significance (May 23, 2024)
6-33293230-G-A		not specified	Uncertain significance (Aug 08, 2022)
6-33293257-C-G			Benign (Jan 19, 2018)
6-33293423-C-T		not specified	Uncertain significance (Jun 24, 2022)
6-33293424-G-A		not specified	Uncertain significance (Mar 31, 2024)
6-33293462-C-G		not specified	Likely benign (May 03, 2023)
6-33293478-G-A		not specified	Uncertain significance (Jan 19, 2024)
6-33293495-G-A		not specified	Uncertain significance (Jan 02, 2024)
6-33293495-G-C		not specified	Uncertain significance (Jan 19, 2024)
6-33293498-G-A		not specified	Uncertain significance (May 11, 2022)
6-33293634-C-T		not specified	Uncertain significance (Jan 30, 2024)
6-33293643-C-T		not specified	Uncertain significance (Dec 27, 2022)
6-33293649-G-C		not specified	Uncertain significance (Nov 27, 2023)
6-33293816-C-T		not specified	Likely benign (Oct 26, 2021)
6-33293853-G-A		not specified	Uncertain significance (Apr 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RGL2	protein_coding	protein_coding	ENST00000497454	17	7671

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0270	0.973	125716	0	32	125748	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.97	351	471	0.745	0.0000292	4888
Missense in Polyphen		150	224.19	0.66907		2337
Synonymous	2.98	138	190	0.725	0.0000106	1765
Loss of Function	4.29	11	40.5	0.272	0.00000256	399

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000871	0.0000871
Ashkenazi Jewish	0.000992	0.000993
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000116	0.000114
Middle Eastern	0.000109	0.000109
South Asian	0.000104	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable guanine nucleotide exchange factor. Putative effector of Ras and/or Rap. Associates with the GTP-bound form of Rap 1A and H-Ras in vitro (By similarity). {ECO:0000250}.
• Pathway: Ras signaling pathway - Homo sapiens (human);Ras Signaling (Consensus)

Intolerance Scores

• loftool: 0.706
• rvis_EVS: -0.69
• rvis_percentile_EVS: 15.27

Haploinsufficiency Scores

• pHI: 0.227
• hipred: Y
• hipred_score: 0.520
• ghis: 0.501

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.543

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rgl2

Gene ontology

• Biological process: Ras protein signal transduction;negative regulation of cardiac muscle cell apoptotic process;positive regulation of phosphatidylinositol 3-kinase signaling;regulation of Ral protein signal transduction
• Cellular component: cellular_component
• Molecular function: Ras guanyl-nucleotide exchange factor activity;Rho guanyl-nucleotide exchange factor activity;protein binding