ARHGEF11

Rho guanine nucleotide exchange factor 11, the group of MicroRNA protein coding host genes|PDZ domain containing|Dbl family Rho GEFs

Basic information

Region (hg38): 1:156934840-157046903

Links

ENSG00000132694 ∙ NCBI:9826 ∙ OMIM:605708 ∙ HGNC:14580 ∙ Uniprot:O15085 ∙ 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 ARHGEF11 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARHGEF11 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	1	3
missense			59	4		63
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	59	6	1

Variants in ARHGEF11

This is a list of pathogenic ClinVar variants found in the ARHGEF11 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-156936869-G-A		not specified	Uncertain significance (Nov 23, 2021)
1-156936926-A-G		not specified	Uncertain significance (Sep 27, 2021)
1-156936941-G-A		not specified	Uncertain significance (Dec 15, 2023)
1-156936966-C-G		not specified	Uncertain significance (Aug 17, 2022)
1-156936993-C-T		not specified	Uncertain significance (Dec 27, 2022)
1-156937271-G-A		not specified	Uncertain significance (Dec 15, 2023)
1-156937286-G-T		not specified	Uncertain significance (Jan 23, 2024)
1-156937299-T-C		not specified	Uncertain significance (Aug 29, 2022)
1-156937311-T-C		not specified	Uncertain significance (Apr 07, 2023)
1-156937334-C-T		not specified	Uncertain significance (Jan 04, 2022)
1-156937340-G-A		not specified	Likely benign (Dec 09, 2023)
1-156937344-G-A		not specified	Uncertain significance (Jan 05, 2022)
1-156937356-C-T		not specified	Uncertain significance (Mar 16, 2024)
1-156937362-C-A		not specified	Uncertain significance (Aug 02, 2021)
1-156937379-T-G		not specified	Uncertain significance (Oct 03, 2022)
1-156937502-C-G			Likely benign (Mar 28, 2018)
1-156939560-C-T		not specified	Uncertain significance (May 31, 2023)
1-156939630-C-A		not specified	Uncertain significance (Jan 26, 2022)
1-156939658-G-T		not specified	Uncertain significance (Oct 26, 2022)
1-156939704-G-A		not specified	Uncertain significance (Oct 04, 2022)
1-156939772-C-A		not specified	Uncertain significance (Jul 30, 2023)
1-156939797-C-T		not specified	Likely benign (Nov 15, 2021)
1-156939812-G-C		not specified	Uncertain significance (Jan 26, 2022)
1-156939812-G-T		not specified	Uncertain significance (Nov 13, 2023)
1-156939833-C-T		not specified	Uncertain significance (Jun 09, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARHGEF11	protein_coding	protein_coding	ENST00000368194	41	110531

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000141	125725	0	23	125748	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.63	781	920	0.849	0.0000548	10092
Missense in Polyphen		206	288.83	0.71321		3129
Synonymous	2.19	302	354	0.852	0.0000200	3196
Loss of Function	7.65	12	90.5	0.133	0.00000514	971

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000299	0.000298
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000955	0.0000924
European (Non-Finnish)	0.0000794	0.0000791
Middle Eastern	0.0000544	0.0000544
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in the regulation of RhoA GTPase by guanine nucleotide-binding alpha-12 (GNA12) and alpha-13 (GNA13). Acts as guanine nucleotide exchange factor (GEF) for RhoA GTPase and may act as GTPase-activating protein (GAP) for GNA12 and GNA13. Involved in neurotrophin-induced neurite outgrowth. {ECO:0000269|PubMed:21670212}.
• Pathway: Vascular smooth muscle contraction - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Developmental Biology;Signaling by GPCR;Signal Transduction;Rho GTPase cycle;Signaling by Rho GTPases;Sema4D induced cell migration and growth-cone collapse;Sema4D in semaphorin signaling;NRAGE signals death through JNK;Semaphorin interactions;Death Receptor Signalling;p75 NTR receptor-mediated signalling;Axon guidance;G alpha (12/13) signalling events;GPCR downstream signalling;Signaling events mediated by focal adhesion kinase;Cell death signalling via NRAGE, NRIF and NADE;Regulation of RhoA activity (Consensus)

Recessive Scores

• pRec: 0.151

Intolerance Scores

• loftool: 0.371
• rvis_EVS: -1.71
• rvis_percentile_EVS: 2.5

Haploinsufficiency Scores

• pHI: 0.310
• hipred: Y
• hipred_score: 0.586
• ghis: 0.577

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.592

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arhgef11
• Phenotype: pigmentation phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; normal 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype; vision/eye phenotype; 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); adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; homeostasis/metabolism phenotype; cellular phenotype

Zebrafish Information Network

• Gene name: arhgef11
• Affected structure: ventricular system
• Phenotype tag: abnormal
• Phenotype quality: increased size

Gene ontology

• Biological process: regulation of cell growth;striated muscle contraction;G protein-coupled receptor signaling pathway;Rho protein signal transduction;establishment of cell polarity;actin cytoskeleton organization;regulation of Rho protein signal transduction;positive regulation of apoptotic process;positive regulation of GTPase activity;positive regulation of transcription, DNA-templated;regulation of small GTPase mediated signal transduction
• Cellular component: cytoplasm;cytosol;membrane
• Molecular function: G protein-coupled receptor binding;guanyl-nucleotide exchange factor activity;Rho guanyl-nucleotide exchange factor activity;GTPase activator activity;protein binding