ARHGEF17

Rho guanine nucleotide exchange factor 17, the group of Dbl family Rho GEFs

Basic information

Region (hg38): 11:73308275-73369388

Links

ENSG00000110237 ∙ NCBI:9828 ∙ OMIM:617043 ∙ HGNC:21726 ∙ Uniprot:Q96PE2 ∙ 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 ARHGEF17 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARHGEF17 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				6	2	8
missense			124	8	1	133
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	124	14	3

Variants in ARHGEF17

This is a list of pathogenic ClinVar variants found in the ARHGEF17 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-73308662-C-G			Likely benign (Sep 01, 2022)
11-73308682-C-T		not specified	Uncertain significance (Feb 05, 2024)
11-73308688-A-C		not specified	Uncertain significance (Apr 26, 2024)
11-73308733-A-G		not specified	Uncertain significance (Apr 22, 2022)
11-73308759-C-T		not specified	Uncertain significance (Mar 20, 2023)
11-73308768-T-A		not specified	Uncertain significance (Jul 13, 2021)
11-73308838-C-A		not specified	Uncertain significance (Dec 16, 2023)
11-73308840-G-A		not specified	Uncertain significance (Jul 05, 2022)
11-73308852-C-T		not specified	Uncertain significance (Nov 18, 2023)
11-73308870-C-T		not specified	Uncertain significance (Jul 05, 2023)
11-73308877-C-T		not specified	Uncertain significance (Dec 04, 2023)
11-73308898-G-A		not specified	Uncertain significance (Dec 15, 2023)
11-73308934-C-T		not specified	Uncertain significance (Mar 19, 2024)
11-73308978-G-T		not specified	Uncertain significance (Mar 19, 2024)
11-73308979-C-A		not specified	Uncertain significance (Mar 19, 2024)
11-73309011-A-C		not specified	Uncertain significance (Feb 14, 2023)
11-73309055-G-C		not specified	Uncertain significance (Feb 09, 2022)
11-73309093-G-A		not specified	Uncertain significance (Dec 28, 2022)
11-73309116-C-A		not specified	Uncertain significance (Jun 22, 2023)
11-73309122-G-C		not specified	Uncertain significance (Jul 10, 2023)
11-73309163-A-C			Likely benign (Feb 01, 2023)
11-73309176-G-A		not specified	Uncertain significance (Sep 26, 2023)
11-73309226-G-C		not specified	Uncertain significance (Mar 28, 2024)
11-73309254-C-T		not specified	Uncertain significance (Apr 01, 2024)
11-73309298-C-G		not specified	Uncertain significance (Jun 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARHGEF17	protein_coding	protein_coding	ENST00000263674	21	60803

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.984	0.0155	125713	0	33	125746	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.750	1176	1.25e+3	0.940	0.0000790	13131
Missense in Polyphen		334	390.98	0.85426		4268
Synonymous	-1.53	576	531	1.08	0.0000342	4528
Loss of Function	6.66	15	78.8	0.190	0.00000472	799

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000428	0.000428
Ashkenazi Jewish	0.000299	0.000298
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000162	0.000158
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000981	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as guanine nucleotide exchange factor (GEF) for RhoA GTPases. {ECO:0000269|PubMed:12071859}.
• Pathway: Signaling by GPCR;Signal Transduction;Rho GTPase cycle;Signaling by Rho GTPases;NRAGE signals death through JNK;Death Receptor Signalling;p75 NTR receptor-mediated signalling;G alpha (12/13) signalling events;GPCR downstream signalling;Cell death signalling via NRAGE, NRIF and NADE;Regulation of RhoA activity (Consensus)

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.412
• rvis_EVS: -0.75
• rvis_percentile_EVS: 13.75

Haploinsufficiency Scores

• pHI: 0.302
• hipred: Y
• hipred_score: 0.614
• ghis: 0.562

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.620

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arhgef17

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;actin cytoskeleton organization;regulation of Rho protein signal transduction;positive regulation of apoptotic process;regulation of small GTPase mediated signal transduction
• Cellular component: cytosol
• Molecular function: guanyl-nucleotide exchange factor activity;Rho guanyl-nucleotide exchange factor activity