RGL1

ral guanine nucleotide dissociation stimulator like 1

Basic information

Region (hg38): 1:183636084-183928532

Links

ENSG00000143344 ∙ NCBI:23179 ∙ OMIM:605667 ∙ HGNC:30281 ∙ Uniprot:Q9NZL6 ∙ 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 RGL1 gene.

• Inborn genetic diseases (18 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RGL1 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						0
missense			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding			6	1	4	11
Total	0	0	17	1	4

Variants in RGL1

This is a list of pathogenic ClinVar variants found in the RGL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-183647716-C-T		not specified	Uncertain significance (Jan 22, 2024)
1-183647821-T-C			Benign (Dec 31, 2019)
1-183647883-T-C			Benign (Dec 31, 2019)
1-183647916-G-A		not specified	Likely benign (Aug 02, 2023)
1-183648079-C-T		not specified	Uncertain significance (Aug 08, 2022)
1-183648102-T-C		not specified	Uncertain significance (Dec 21, 2023)
1-183648172-C-T		not specified	Uncertain significance (Dec 13, 2022)
1-183648195-G-C			Benign (Dec 31, 2019)
1-183648236-C-T			Benign (Apr 30, 2018)
1-183648259-G-A		not specified	Uncertain significance (Dec 06, 2021)
1-183648268-C-T		not specified	Uncertain significance (Dec 16, 2021)
1-183648499-C-T		not specified	Uncertain significance (Oct 16, 2023)
1-183648609-G-A		not specified	Uncertain significance (Oct 06, 2023)
1-183648675-C-A		not specified	Uncertain significance (Apr 04, 2023)
1-183648690-C-A		not specified	Uncertain significance (Apr 19, 2023)
1-183648703-C-T		not specified	Uncertain significance (Jan 17, 2024)
1-183742191-G-A		not specified	Uncertain significance (Dec 06, 2023)
1-183742193-G-C		not specified	Uncertain significance (Nov 27, 2023)
1-183742219-A-G		not specified	Uncertain significance (Aug 14, 2023)
1-183806457-C-T		not specified	Uncertain significance (Oct 20, 2023)
1-183866018-A-T		not specified	Uncertain significance (May 23, 2023)
1-183880719-C-T		not specified	Uncertain significance (Sep 27, 2021)
1-183883800-A-G		not specified	Uncertain significance (Sep 14, 2022)
1-183883869-T-C		not specified	Uncertain significance (Sep 20, 2023)
1-183883902-A-G		not specified	Uncertain significance (May 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RGL1	protein_coding	protein_coding	ENST00000304685	18	292446

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.956	0.0439	125734	0	14	125748	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.22	315	447	0.704	0.0000242	5292
Missense in Polyphen		68	148.62	0.45755		1821
Synonymous	0.249	168	172	0.976	0.00000994	1523
Loss of Function	5.12	8	45.1	0.178	0.00000231	517

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable guanine nucleotide exchange factor.
• Pathway: Ras signaling pathway - Homo sapiens (human);Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha);Ras Signaling (Consensus)

Recessive Scores

• pRec: 0.141

Intolerance Scores

• loftool: 0.380
• rvis_EVS: -1
• rvis_percentile_EVS: 8.47

Haploinsufficiency Scores

• pHI: 0.244
• hipred: Y
• hipred_score: 0.685
• ghis: 0.575

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.756

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rgl1

Gene ontology

• Biological process: small GTPase mediated signal transduction;regulation of lipid metabolic process
• Cellular component: cellular_component;cytosol
• Molecular function: protein binding;Ral guanyl-nucleotide exchange factor activity