Rapgef1 MGI Mouse Gene Detail - MGI:104580 - Rap guanine nucleotide exchange factor (GEF) 1

Symbol

Rapgef1
Name

Rap guanine nucleotide exchange factor (GEF) 1
Synonyms

4932418O06Rik, C3G, Grf2

Feature Type

protein coding gene
IDs

MGI:104580
NCBI Gene: 107746
Alliance

genome feature page
Transcription Start Sites

11 TSS

Sequence Map

Chr2:29509732-29630376 bp, + strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 2, 20.32 cM, cytoband B
Mapping Data

4 experiments

SNPs within 2kb

2478 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_104580	protein coding gene	Chr2:29509732-29630990 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0025540	protein coding gene	Chr2:27768249-27897250 (+)
A/J	MGP_AJ_G0025517	protein coding gene	Chr2:26689036-26809893 (+)
AKR/J	MGP_AKRJ_G0025487	protein coding gene	Chr2:27582101-27707983 (+)
BALB/cJ	MGP_BALBcJ_G0025513	protein coding gene	Chr2:26820996-26941552 (+)
C3H/HeJ	MGP_C3HHeJ_G0025274	protein coding gene	Chr2:27514897-27639970 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0025957	protein coding gene	Chr2:28660678-28799612 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0023367	protein coding gene	Chr2:25483148-25602703 (+)
CAST/EiJ	MGP_CASTEiJ_G0024737	protein coding gene	Chr2:27410358-27532992 (+)
CBA/J	MGP_CBAJ_G0025252	protein coding gene	Chr2:29655924-29787450 (+)
DBA/2J	MGP_DBA2J_G0025385	protein coding gene	Chr2:26487492-26608721 (+)
FVB/NJ	MGP_FVBNJ_G0025347	protein coding gene	Chr2:26286894-26411977 (+)
LP/J	MGP_LPJ_G0025471	protein coding gene	Chr2:27694520-27826321 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0025378	protein coding gene	Chr2:29605441-29737334 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0026016	protein coding gene	Chr2:27498092-27631201 (+)
PWK/PhJ	MGP_PWKPhJ_G0024484	protein coding gene	Chr2:26310512-26434295 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0024284	protein coding gene	Chr2:27595027-27715756 (+)
WSB/EiJ	MGP_WSBEiJ_G0024806	protein coding gene	Chr2:27630017-27755230 (+)

Human Ortholog

RAPGEF1, Rap guanine nucleotide exchange factor 1

Vertebrate Orthologs

4

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

RAPGEF1, Rap guanine nucleotide exchange factor 1
Synonyms

C3G, GRF2
Links

HGNC:4568

NCBI Gene ID: 2889

UniProt: Q13905
Chr Location

9q34.13; chr9:131576758-131740117 (-) GRCh38

MGI Vertebrate Homology

Rapgef1 stringent orthology
1 human;1 mouse;1 rat;2 zebrafish
HCOP

vertebrate homology predictions: RAPGEF1
Gene Tree

Rapgef1

less

Phenotype Summary

13 phenotypes from 3 alleles in 4 genetic backgrounds
22 phenotype references

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

adipose tissue	behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary system	embryo	endocrine/exocrine glands	growth/size/body	hearing/vestibular/ear	hematopoietic system	homeostasis/metabolism	integument	immune system	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	neoplasm	vision/eye

Click cells to view annotations.

All Mutations and Alleles

199
Endonuclease-mediated

1
Gene trapped

193
Targeted

5
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

192 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for a null allele die before E7.5. Mice homozygous for a hypomorphic gene trap allele show embryonic lethality during organogenesis, altered neuroepithelium morphology, vascular maturation defects, hemorrhage, and reduced cell migration and adhesion.

less

Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

983
Tissues

78
cDNA Data

197
Literature Summary

13

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

GEISHA RAPGEF1

Xenbase rapgef1

ZFIN rapgef1b

less

All Sequences

118
RefSeq

54
UniProt

14
CCDS

CCDS15854.1, CCDS38091.1, CCDS38092.1, CCDS89458.1

Ensembl

ENSMUSG00000039844 (Evidence)
NCBI Gene

107746

			Length	Strain/Species	Flank
genomic	107746	NCBI Gene Model \| MGI Sequence Detail	120645	C57BL/6J	± kb
transcript	NM_001039086	RefSeq \| MGI Sequence Detail	6233	ZRU/MplStud
polypeptide	NP_001034176	RefSeq \| MGI Sequence Detail	1224	C57BL/6

less

UniProt

14 Sequences
Protein Ontology

PR:000013726 Rap guanine nucleotide exchange factor 1

(term hierarchy)
InterPro Domains

IPR036964 Ras guanine-nucleotide exchange factor, catalytic domain superfamily

IPR019804 Ras guanine-nucleotide exchange factor, conserved site

IPR023578 Ras guanine nucleotide exchange factor domain superfamily

IPR001895 Ras guanine-nucleotide exchange factors catalytic domain

IPR008937 Ras-like guanine nucleotide exchange factor

IPR000651 Ras-like guanine nucleotide exchange factor, N-terminal
GlyGen

A0A5F8MPI9 3 sites, 4 N-linked glycans (3 sites)

less

All nucleic 207

cDNA 197

Primer pair 9

Other 1

Antibodies 2

Microarray probesets 5

less

MGD-MRK-26014, MGI:2444538

Summaries

All 75

Developmental Gene Expression 13

Phenotypes 22
Earliest

J:26202 Schumacher C, et al., The SH3 domain of Crk binds specifically to a conserved proline-rich motif in Eps15 and Eps15R. J Biol Chem. 1995 Jun 23;270(25):15341-7
Latest

J:374271 Palao N, et al., Deletion of C3G in hepatocytes impairs full liver maturation and alters glucose homeostasis. Cell Death Dis. 2025 Oct 7;16(1):711

TSS for Rapgef1:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr17004	Chr2:29509704-29509837 (+)	39 bp
Tssr17005	Chr2:29511448-29511472 (+)	1,728 bp
Tssr17006	Chr2:29515072-29515084 (+)	5,346 bp
Tssr17007	Chr2:29519767-29519776 (+)	10,040 bp
Tssr17008	Chr2:29533677-29533693 (+)	23,953 bp
Tssr17009	Chr2:29533710-29533724 (+)	23,985 bp
Tssr17010	Chr2:29533750-29533769 (+)	24,028 bp
Tssr17011	Chr2:29533775-29533794 (+)	24,053 bp
Tssr17012	Chr2:29533800-29533817 (+)	24,077 bp
Tssr17013	Chr2:29589799-29589820 (+)	80,078 bp
Tssr17014	Chr2:29614039-29614041 (+)	104,308 bp

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
Citing These Resources Funding Information Warranty Disclaimer, Privacy Notice, Licensing, & Copyright Send questions and comments to User Support.	last database update 06/09/2026 MGI 6.24