RGL4

ral guanine nucleotide dissociation stimulator like 4

Basic information

Region (hg38): 22:23688135-23699176

Links

ENSG00000159496 ∙ NCBI:266747 ∙ OMIM:612214 ∙ HGNC:31911 ∙ Uniprot:Q8IZJ4 ∙ 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 RGL4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RGL4 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			28	3		31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	4	0

Variants in RGL4

This is a list of pathogenic ClinVar variants found in the RGL4 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-23692166-T-C		not specified	Likely benign (Apr 22, 2022)
22-23692206-T-C		not specified	Uncertain significance (Oct 03, 2022)
22-23692208-C-T		not specified	Uncertain significance (Nov 14, 2023)
22-23692403-G-A		not specified	Uncertain significance (Nov 28, 2023)
22-23692414-C-T		not specified	Likely benign (Dec 20, 2023)
22-23692491-G-C		not specified	Uncertain significance (Mar 28, 2024)
22-23692695-G-A		not specified	Uncertain significance (Dec 21, 2023)
22-23692782-G-C		not specified	Uncertain significance (Apr 25, 2022)
22-23692828-C-T		not specified	Uncertain significance (Feb 06, 2024)
22-23692855-T-C		not specified	Uncertain significance (Apr 04, 2023)
22-23692882-C-T		not specified	Uncertain significance (May 09, 2023)
22-23692990-C-T		not specified	Uncertain significance (Aug 02, 2021)
22-23693775-T-C		not specified	Uncertain significance (Mar 11, 2024)
22-23693813-G-C		not specified	Likely benign (Apr 22, 2022)
22-23693831-G-A		not specified	Uncertain significance (Aug 10, 2021)
22-23693907-T-C		not specified	Uncertain significance (Nov 06, 2023)
22-23693931-G-A		not specified	Uncertain significance (May 17, 2023)
22-23693970-C-T		not specified	Uncertain significance (Jun 28, 2023)
22-23694349-G-C		not specified	Uncertain significance (Nov 13, 2023)
22-23694432-C-T		not specified	Uncertain significance (Jun 02, 2024)
22-23694960-A-G		not specified	Uncertain significance (Oct 06, 2023)
22-23694963-G-C		not specified	Uncertain significance (Apr 22, 2022)
22-23694982-A-G		not specified	Uncertain significance (Oct 29, 2021)
22-23694985-A-C		not specified	Uncertain significance (Feb 22, 2023)
22-23694991-C-T		not specified	Uncertain significance (Apr 22, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RGL4	protein_coding	protein_coding	ENST00000290691	11	11041

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.14e-13	0.0662	125516	2	230	125748	0.000923

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.276	285	272	1.05	0.0000152	3049
Missense in Polyphen		58	50.665	1.1448		683
Synonymous	-0.676	124	115	1.08	0.00000681	983
Loss of Function	0.436	20	22.2	0.900	0.00000103	254

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000812	0.000812
Ashkenazi Jewish	0.00774	0.00767
East Asian	0.000870	0.000870
Finnish	0.00	0.00
European (Non-Finnish)	0.000644	0.000642
Middle Eastern	0.000870	0.000870
South Asian	0.000883	0.000850
Other	0.00196	0.00196

dbNSFP

Source: dbNSFP

• Pathway: GPCRs, Class A Rhodopsin-like (Consensus)

Recessive Scores

• pRec: 0.0571

Intolerance Scores

• loftool: 0.948
• rvis_EVS: 2.56
• rvis_percentile_EVS: 98.74

Haploinsufficiency Scores

• pHI: 0.0202
• hipred: N
• hipred_score: 0.252
• ghis: 0.394

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.417

Gene Damage Prediction

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

Gene ontology

• Biological process: small GTPase mediated signal transduction
• Cellular component: cytoplasmic vesicle
• Molecular function: guanyl-nucleotide exchange factor activity