ARHGEF16

Rho guanine nucleotide exchange factor 16, the group of Dbl family Rho GEFs|Pleckstrin homology domain containing

Basic information

Region (hg38): 1:3454665-3481113

Links

ENSG00000130762 ∙ NCBI:27237 ∙ OMIM:618871 ∙ HGNC:15515 ∙ Uniprot:Q5VV41 ∙ 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 ARHGEF16 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARHGEF16 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					1	1
missense			58	2	1	61
nonsense						0
start loss			1			1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1		1	2
Total	0	0	60	2	3

Variants in ARHGEF16

This is a list of pathogenic ClinVar variants found in the ARHGEF16 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-3463095-G-A		not specified	Uncertain significance (Jun 14, 2023)
1-3463136-C-T		not specified	Uncertain significance (Jun 21, 2023)
1-3463137-G-A		not specified	Uncertain significance (Mar 02, 2023)
1-3463169-G-C		not specified	Uncertain significance (Feb 28, 2023)
1-3463200-G-A		not specified	Uncertain significance (Aug 17, 2022)
1-3463209-C-T		not specified	Likely benign (Mar 19, 2024)
1-3463325-C-G		not specified	Uncertain significance (Mar 07, 2023)
1-3463380-C-T		not specified	Uncertain significance (Dec 08, 2023)
1-3463439-C-T		not specified	Uncertain significance (Oct 10, 2023)
1-3463476-C-A		not specified	Uncertain significance (Jun 02, 2023)
1-3463508-G-A		not specified	Uncertain significance (Feb 23, 2023)
1-3463547-C-T		not specified	Uncertain significance (Mar 02, 2023)
1-3463548-G-A		not specified	Uncertain significance (Jun 09, 2022)
1-3463653-G-A		not specified	Uncertain significance (Nov 23, 2021)
1-3463659-C-T		not specified	Uncertain significance (Jun 18, 2024)
1-3467242-G-A		not specified	Uncertain significance (Jan 19, 2024)
1-3467252-G-C		not specified	Uncertain significance (Oct 05, 2023)
1-3467297-G-C		not specified	Uncertain significance (Dec 15, 2023)
1-3467302-C-T		not specified	Uncertain significance (Jul 05, 2022)
1-3467303-G-A		not specified	Uncertain significance (Mar 06, 2023)
1-3467332-C-T		not specified	Uncertain significance (Jun 02, 2024)
1-3468886-G-A		not specified	Uncertain significance (Oct 10, 2023)
1-3468917-A-G		not specified	Uncertain significance (Jun 12, 2023)
1-3469437-T-C		not specified	Uncertain significance (Mar 31, 2023)
1-3469442-G-A		not specified	Uncertain significance (Dec 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARHGEF16	protein_coding	protein_coding	ENST00000378378	14	26688

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.71e-13	0.536	125393	0	113	125506	0.000450

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.456	411	438	0.939	0.0000302	4618
Missense in Polyphen		159	176.61	0.90028		1665
Synonymous	-0.337	195	189	1.03	0.0000136	1432
Loss of Function	1.47	24	33.1	0.724	0.00000166	364

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000855	0.000852
Ashkenazi Jewish	0.00240	0.00239
East Asian	0.000382	0.000381
Finnish	0.0000465	0.0000462
European (Non-Finnish)	0.000368	0.000362
Middle Eastern	0.000382	0.000381
South Asian	0.000327	0.000327
Other	0.000493	0.000490

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Guanyl-nucleotide exchange factor of the RHOG GTPase stimulating the exchange of RHOG-associated GDP for GTP. May play a role in chemotactic cell migration by mediating the activation of RAC1 by EPHA2. May also activate CDC42 and mediate activation of CDC42 by the viral protein HPV16 E6. {ECO:0000269|PubMed:20679435}.
• 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 (Consensus)

Recessive Scores

• pRec: 0.141

Intolerance Scores

• loftool: 0.808
• rvis_EVS: 0.25
• rvis_percentile_EVS: 69.57

Haploinsufficiency Scores

• pHI: 0.162
• hipred: N
• hipred_score: 0.229
• ghis: 0.487

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.755

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arhgef16

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;regulation of Rho protein signal transduction;positive regulation of apoptotic process;regulation of small GTPase mediated signal transduction;cell chemotaxis;activation of GTPase activity;positive regulation of protein localization to plasma membrane
• Cellular component: cytosol
• Molecular function: guanyl-nucleotide exchange factor activity;Rho guanyl-nucleotide exchange factor activity;protein binding;Rho GTPase binding;PDZ domain binding;receptor tyrosine kinase binding;cadherin binding