RABGEF1

RAB guanine nucleotide exchange factor 1, the group of VPS9 domain containing

Basic information

Region (hg38): 7:66682164-66811464

Links

ENSG00000154710 ∙ NCBI:27342 ∙ OMIM:609700 ∙ HGNC:17676 ∙ Uniprot:Q9UJ41 ∙ 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 RABGEF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RABGEF1 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				2		2
missense			17	1		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	3	0

Variants in RABGEF1

This is a list of pathogenic ClinVar variants found in the RABGEF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-66772073-G-A			Likely benign (Jun 26, 2018)
7-66775288-C-T		not specified	Uncertain significance (Apr 08, 2024)
7-66775364-G-T		not specified	Uncertain significance (Jun 30, 2023)
7-66783686-G-A		not specified	Uncertain significance (Apr 12, 2023)
7-66783735-A-T		not specified	Uncertain significance (Jun 22, 2021)
7-66783831-A-G		not specified	Uncertain significance (Mar 12, 2024)
7-66795577-C-G		not specified	Uncertain significance (Jun 24, 2022)
7-66799340-C-T		not specified	Uncertain significance (Jul 06, 2021)
7-66799366-A-G		not specified	Uncertain significance (Jan 19, 2022)
7-66805173-G-A		not specified	Uncertain significance (Jul 05, 2022)
7-66805187-T-G		not specified	Uncertain significance (Jul 19, 2022)
7-66805218-A-G			Likely benign (May 31, 2018)
7-66805224-T-A		not specified	Uncertain significance (Nov 03, 2023)
7-66805283-A-G		not specified	Uncertain significance (Oct 10, 2023)
7-66805336-G-C			Likely benign (May 17, 2018)
7-66805337-C-T		not specified	Uncertain significance (Dec 18, 2023)
7-66808955-C-T		not specified	Uncertain significance (Jan 19, 2024)
7-66808979-C-T		not specified	Uncertain significance (Jun 23, 2023)
7-66809005-G-T		not specified	Uncertain significance (Oct 13, 2021)
7-66809040-A-G		not specified	Uncertain significance (Nov 18, 2023)
7-66809097-A-C		not specified	Uncertain significance (May 15, 2024)
7-66809181-T-C		not specified	Uncertain significance (Apr 28, 2022)
7-66809216-A-G		not specified	Uncertain significance (May 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RABGEF1	protein_coding	protein_coding	ENST00000284957	8	129301

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000631	0.999	125736	0	10	125746	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.47	210	279	0.753	0.0000158	3274
Missense in Polyphen		20	64.958	0.30789		772
Synonymous	0.754	91	101	0.904	0.00000596	875
Loss of Function	2.90	10	25.9	0.385	0.00000149	296

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.0000721	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Rab effector protein acting as linker between gamma- adaptin, RAB4A or RAB5A. Involved in endocytic membrane fusion and membrane trafficking of recycling endosomes. Stimulates nucleotide exchange on RAB5A. Can act as a ubiquitin ligase (By similarity). {ECO:0000250, ECO:0000269|PubMed:11452015, ECO:0000269|PubMed:15339665, ECO:0000269|PubMed:9323142}.
• Pathway: Regulation of Ras family activation;Vesicle-mediated transport;TBC/RABGAPs;Membrane Trafficking;Rab regulation of trafficking;RAB GEFs exchange GTP for GDP on RABs (Consensus)

Recessive Scores

• pRec: 0.0840

Intolerance Scores

• rvis_EVS: -0.43
• rvis_percentile_EVS: 25.37

Haploinsufficiency Scores

• pHI: 0.165
• hipred: Y
• hipred_score: 0.620
• ghis: 0.487

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• gene_indispensability_pred: E
• gene_indispensability_score: 0.888

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

Mouse Genome Informatics

• Gene name: Rabgef1
• Phenotype: 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); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); immune system phenotype; hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Zebrafish Information Network

• Gene name: rabgef1
• Affected structure: pronephric glomerulus
• Phenotype tag: abnormal
• Phenotype quality: permeability

Gene ontology

• Biological process: protein targeting to membrane;endocytosis
• Cellular component: nucleolus;early endosome;cytosol;early endosome membrane;recycling endosome
• Molecular function: DNA binding;protein binding;zinc ion binding;Rab guanyl-nucleotide exchange factor activity;Rab GTPase binding