ARHGEF7

Rho guanine nucleotide exchange factor 7, the group of Pleckstrin homology domain containing|Dbl family Rho GEFs

Basic information

Region (hg38): 13:111114559-111305737

Links

ENSG00000102606 ∙ NCBI:8874 ∙ OMIM:605477 ∙ HGNC:15607 ∙ Uniprot:Q14155 ∙ 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 ARHGEF7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARHGEF7 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				4	10	14
missense			30	2	1	33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding			3			3
Total	0	0	33	6	11

Variants in ARHGEF7

This is a list of pathogenic ClinVar variants found in the ARHGEF7 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-111115566-C-T			Likely benign (Dec 31, 2019)
13-111115611-G-A			Likely benign (Dec 26, 2018)
13-111115672-T-G		not specified	Uncertain significance (Apr 20, 2023)
13-111153917-C-G		not specified	Uncertain significance (Aug 30, 2021)
13-111153926-G-C		not specified	Uncertain significance (Jan 10, 2022)
13-111153930-G-T		not specified	Uncertain significance (Jan 23, 2024)
13-111159083-T-G			Likely benign (Jun 05, 2018)
13-111205290-C-T		not specified	Uncertain significance (Aug 14, 2023)
13-111205296-A-C		not specified	Uncertain significance (May 15, 2024)
13-111205352-A-G		not specified	Uncertain significance (May 08, 2024)
13-111209902-C-T		not specified	Uncertain significance (Mar 02, 2023)
13-111209904-C-G		not specified	Uncertain significance (Dec 28, 2023)
13-111209940-C-T		not specified	Uncertain significance (Jul 14, 2022)
13-111209964-C-T		not specified	Uncertain significance (Oct 05, 2023)
13-111209994-C-T		not specified	Uncertain significance (Mar 29, 2022)
13-111209997-A-T			Likely benign (Dec 31, 2019)
13-111217707-T-G		not specified	Uncertain significance (Jun 22, 2021)
13-111217764-C-T		not specified	Uncertain significance (Oct 26, 2021)
13-111217791-G-A		not specified	Uncertain significance (Jan 04, 2024)
13-111217801-G-C			Benign (Dec 31, 2019)
13-111217867-G-C		not specified	Uncertain significance (May 15, 2024)
13-111217879-C-T			Benign (Dec 31, 2019)
13-111233210-C-G		not specified	Uncertain significance (Jul 12, 2023)
13-111233214-T-C		not specified	Uncertain significance (Oct 06, 2021)
13-111243936-C-T		not specified	Uncertain significance (Jul 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARHGEF7	protein_coding	protein_coding	ENST00000375741	20	191179

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000461	125742	0	6	125748	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.57	313	470	0.666	0.0000278	5214
Missense in Polyphen		90	174.92	0.51452		1863
Synonymous	0.197	186	189	0.982	0.0000120	1550
Loss of Function	5.54	3	41.5	0.0723	0.00000184	527

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000546	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000363	0.0000352
Middle Eastern	0.0000546	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a RAC1 guanine nucleotide exchange factor (GEF) and can induce membrane ruffling. Functions in cell migration, attachment and cell spreading. Promotes targeting of RAC1 to focal adhesions (By similarity). May function as a positive regulator of apoptosis. Downstream of NMDA receptors and CaMKK-CaMK1 signaling cascade, promotes the formation of spines and synapses in hippocampal neurons. {ECO:0000250, ECO:0000269|PubMed:18184567, ECO:0000269|PubMed:18716323, ECO:0000269|PubMed:19041750}.
• Pathway: Regulation of actin cytoskeleton - Homo sapiens (human);Intracellular Signalling Through Adenosine Receptor A2b and Adenosine;Intracellular Signalling Through Adenosine Receptor A2a and Adenosine;Integrin-mediated Cell Adhesion;Regulation of Actin Cytoskeleton;Developmental Biology;Signaling by GPCR;Signal Transduction;EPH-Ephrin signaling;TCR;Ephrin signaling;Rho GTPase cycle;Aurora A signaling;EGFR downregulation;Signaling by EGFR;Signaling by Rho GTPases;EGFR1;agrin in postsynaptic differentiation;Regulation of RAC1 activity;NRAGE signals death through JNK;Death Receptor Signalling;p75 NTR receptor-mediated signalling;Axon guidance;G alpha (12/13) signalling events;Integrin-linked kinase signaling;Signaling by Receptor Tyrosine Kinases;GPCR downstream signalling;Regulation of CDC42 activity;CDC42 signaling events;Internalization of ErbB1;Signaling events mediated by focal adhesion kinase;Cell death signalling via NRAGE, NRIF and NADE (Consensus)

Recessive Scores

• pRec: 0.624

Intolerance Scores

• loftool: 0.444
• rvis_EVS: -1.04
• rvis_percentile_EVS: 7.8

Haploinsufficiency Scores

• pHI: 0.224
• hipred: Y
• hipred_score: 0.745
• ghis: 0.577

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.894

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arhgef7
• 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); homeostasis/metabolism phenotype

Zebrafish Information Network

• Gene name: arhgef7b
• Affected structure: leukocyte
• Phenotype tag: abnormal
• Phenotype quality: accumulation

Gene ontology

• Biological process: hematopoietic progenitor cell differentiation;Golgi organization;signal transduction;G protein-coupled receptor signaling pathway;nervous system development;positive regulation of fibroblast migration;lamellipodium assembly;positive regulation of protein binding;regulation of Rho protein signal transduction;intracellular signal transduction;negative regulation of epidermal growth factor receptor signaling pathway;positive regulation of apoptotic process;positive regulation of GTPase activity;ephrin receptor signaling pathway;focal adhesion assembly;regulation of small GTPase mediated signal transduction;positive regulation of growth hormone secretion;positive regulation of substrate adhesion-dependent cell spreading;regulation of GTP binding;positive regulation of lamellipodium morphogenesis
• Cellular component: storage vacuole;ruffle;cytosol;plasma membrane;focal adhesion;cell cortex;lamellipodium;protein-containing complex;neuron projection;neuronal cell body
• Molecular function: guanyl-nucleotide exchange factor activity;Rho guanyl-nucleotide exchange factor activity;protein binding;protein kinase binding