RAPGEFL1

protein-coding

Rap guanine nucleotide exchange factor like 1, the group of MicroRNA protein coding host genes

Gene summary

Predicted to enable guanyl-nucleotide exchange factor activity. Predicted to be involved in Rap protein signal transduction. Predicted to be located in membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_016339.6

Inheritance

—

ClinVar variants

U:51B:2

Top phenotype

Prostate cancer

gnomAD constraint

pLI —, LoF o/e 0.23

Max pathogenic AF

—

Genomic locus

chr17:40,177,010-40,195,656

External References & Databases

Ensembl (ENSG00000108352)

Transcript & Mutation Effects

hg38 • Region Span ~18.6 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 RAPGEFL1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 48

Prostate cancerTotal: 1

Familial cold autoinflammatory syndrome 2Total: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016339.6. 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				1 clinvar		1
missense			48 clinvar	1 clinvar		49
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	51	2	0	53

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 18 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016339.6	RefSeq	NP_057423.2	15	MANE Select
ENST00000620260.6	Ensembl	ENSP00000479735.1	15	MANE Select
NM_001303533.2	RefSeq	NP_001290462.1	15	Standard
NM_001303534.3	RefSeq	NP_001290463.1	15	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

G protein-coupled receptor signaling pathway
small GTPase mediated signal transduction
nervous system development

Molecular Function

guanyl-nucleotide exchange factor activity

Cellular Component

membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000436615
Coding exons: 13
Length: 18646
Individuals with no LoFs: 125735
Homozygous LoFs: 0
Heterozygous LoFs: 13
Defined: 125748
p: 0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.76	186	267	0.697	0.0000156	2940
Missense (PolyPhen)		47	68.67	0.68443		789
Synonymous	0.510	100	107	0.937	0.00000584	903
Loss of Function	3.60	6	25.7	0.233	0.00000132	286

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.000065	0.000062	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 (GEF).;

Intolerance Scores

LoFtool: 0.486
RVIS EVS: -0.76
RVIS percentile EVS: 13.33

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.314

Gene Damage Prediction

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