RAPGEFL1

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

Basic information

Region (hg38): 17:40177010-40195656

Links

ENSG00000108352 ∙ NCBI:51195 ∙ ∙ HGNC:17428 ∙ Uniprot:Q9UHV5 ∙ 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 RAPGEFL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAPGEFL1 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			20	1		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	1	0

Variants in RAPGEFL1

This is a list of pathogenic ClinVar variants found in the RAPGEFL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-40184257-C-T		not specified	Uncertain significance (Aug 12, 2021)
17-40184320-G-C		not specified	Uncertain significance (Apr 04, 2024)
17-40184653-C-A		not specified	Uncertain significance (Jun 28, 2022)
17-40188883-A-G		Malignant tumor of prostate	Uncertain significance (-)
17-40188889-C-T		not specified	Uncertain significance (Jan 16, 2024)
17-40188927-C-T		not specified	Uncertain significance (Nov 06, 2023)
17-40189318-G-C		not specified	Uncertain significance (Oct 26, 2022)
17-40189320-G-T		not specified	Uncertain significance (Jun 24, 2022)
17-40189327-G-A		not specified	Uncertain significance (Dec 15, 2023)
17-40189328-C-T		not specified	Uncertain significance (Sep 20, 2023)
17-40189333-C-T		not specified	Uncertain significance (Jan 19, 2022)
17-40190461-A-G		not specified	Uncertain significance (Feb 27, 2023)
17-40190691-C-T		Familial cold autoinflammatory syndrome 2	Uncertain significance (Oct 19, 2017)
17-40190704-A-G		not specified	Uncertain significance (Feb 22, 2023)
17-40190758-A-C		not specified	Uncertain significance (Oct 05, 2021)
17-40190759-T-G		not specified	Uncertain significance (Oct 05, 2021)
17-40191458-C-T		not specified	Uncertain significance (Aug 02, 2022)
17-40191595-C-G		not specified	Uncertain significance (Jul 14, 2022)
17-40191601-C-G		not specified	Uncertain significance (Nov 03, 2022)
17-40191643-G-A		not specified	Uncertain significance (Feb 28, 2023)
17-40192972-G-A		not specified	Likely benign (Apr 12, 2024)
17-40193390-A-G		not specified	Likely benign (Aug 17, 2022)
17-40193415-T-G		not specified	Uncertain significance (May 09, 2022)
17-40193688-A-G		not specified	Uncertain significance (Aug 12, 2021)
17-40193733-A-G		not specified	Uncertain significance (Feb 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAPGEFL1	protein_coding	protein_coding	ENST00000436615	13	18646

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.297	0.703	125735	0	13	125748	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.76	186	267	0.697	0.0000156	2940
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000139	0.000139
European (Non-Finnish)	0.0000647	0.0000615
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 (GEF).

Intolerance Scores

• loftool: 0.486
• rvis_EVS: -0.76
• rvis_percentile_EVS: 13.33

Haploinsufficiency Scores

• pHI: 0.425
• hipred: Y
• hipred_score: 0.622
• ghis: 0.623

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.314

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rapgefl1
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;small GTPase mediated signal transduction;nervous system development
• Cellular component: membrane
• Molecular function: guanyl-nucleotide exchange factor activity