RGL1

protein-coding

ral guanine nucleotide dissociation stimulator like 1

Gene summary

Predicted to enable guanyl-nucleotide exchange factor activity. Predicted to be involved in Ras protein signal transduction. Predicted to be located in cytosol. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001297671.3

Inheritance

—

ClinVar variants

U:77B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.18

Max pathogenic AF

—

Genomic locus

chr1:183,636,085-183,928,532

External References & Databases

Ensembl (ENSG00000143344)

Transcript & Mutation Effects

hg38 • Region Span ~292.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to RGL1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 64

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001297671.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			3 clinvar	1 clinvar		4
missense			66 clinvar			66
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	77	1	0	78

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 34 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001297671.3	RefSeq	NP_001284600.1	18	MANE Select
ENST00000360851.4	Ensembl	ENSP00000354097.3	18	MANE Select
NM_001297669.3	RefSeq	NP_001284598.1	17	Standard
NM_001297670.3	RefSeq	NP_001284599.1	17	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Ras signaling pathway - Homo sapiens (human)
Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha)
Ras Signaling

Biological Process

small GTPase mediated signal transduction
regulation of lipid metabolic process

Molecular Function

protein binding
Ral guanyl-nucleotide exchange factor activity

Cellular Component

cellular_component
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000304685
Coding exons: 18
Length: 292446
Individuals with no LoFs: 125734
Homozygous LoFs: 0
Heterozygous LoFs: 14
Defined: 125748
p: 0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.22	315	447	0.704	0.0000242	5292
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.00011	0.00011	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Probable guanine nucleotide exchange factor.;

Recessive Scores

pRec: 0.141

Intolerance Scores

LoFtool: 0.380
RVIS EVS: -1
RVIS percentile EVS: 8.47

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.756

Gene Damage Prediction

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