ARHGEF19

Rho guanine nucleotide exchange factor 19, the group of Dbl family Rho GEFs

Basic information

Region (hg38): 1:16197854-16212652

Links

ENSG00000142632 ∙ NCBI:128272 ∙ OMIM:612496 ∙ HGNC:26604 ∙ Uniprot:Q8IW93 ∙ 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 ARHGEF19 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARHGEF19 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			50	4	1	55
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	50	5	1

Variants in ARHGEF19

This is a list of pathogenic ClinVar variants found in the ARHGEF19 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-16198635-A-T		not specified	Uncertain significance (Feb 17, 2022)
1-16199206-T-C		not specified	Uncertain significance (Dec 28, 2022)
1-16199251-C-T		not specified	Uncertain significance (Mar 06, 2023)
1-16201799-A-G		not specified	Uncertain significance (Dec 26, 2023)
1-16201847-C-T		not specified	Uncertain significance (Apr 25, 2023)
1-16202423-G-A		not specified	Uncertain significance (Apr 19, 2023)
1-16202429-G-A		not specified	Uncertain significance (Dec 28, 2023)
1-16202444-G-A		not specified	Uncertain significance (May 04, 2023)
1-16202459-C-T		not specified	Uncertain significance (May 31, 2023)
1-16202552-C-T		not specified	Uncertain significance (Apr 15, 2024)
1-16204766-G-A		not specified	Uncertain significance (Sep 28, 2022)
1-16204768-C-T			Benign (Mar 29, 2018)
1-16204804-T-C		not specified	Uncertain significance (Jun 03, 2024)
1-16204876-C-G		not specified	Uncertain significance (Jan 03, 2024)
1-16205100-T-C		not specified	Uncertain significance (Dec 19, 2022)
1-16205565-C-G		not specified	Uncertain significance (Jul 05, 2022)
1-16205633-G-A		not specified	Uncertain significance (Mar 14, 2023)
1-16205652-C-A		not specified	Uncertain significance (May 16, 2024)
1-16205939-C-A		not specified	Uncertain significance (Aug 02, 2021)
1-16206000-G-A		not specified	Uncertain significance (Apr 12, 2022)
1-16206054-T-A		not specified	Uncertain significance (Oct 20, 2021)
1-16206189-G-A		not specified	Uncertain significance (Sep 16, 2021)
1-16206328-G-C		not specified	Uncertain significance (Feb 26, 2024)
1-16206964-T-G		not specified	Uncertain significance (Apr 11, 2023)
1-16206989-C-T		not specified	Uncertain significance (Aug 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARHGEF19	protein_coding	protein_coding	ENST00000270747	15	14756

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.95e-20	0.0180	125666	0	81	125747	0.000322

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.965	401	459	0.873	0.0000284	5052
Missense in Polyphen		125	170.22	0.73435		1802
Synonymous	1.51	162	188	0.860	0.0000105	1694
Loss of Function	0.799	33	38.3	0.861	0.00000200	415

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000806	0.000763
Ashkenazi Jewish	0.000299	0.000298
East Asian	0.000163	0.000163
Finnish	0.0000984	0.0000924
European (Non-Finnish)	0.000409	0.000396
Middle Eastern	0.000163	0.000163
South Asian	0.000298	0.000294
Other	0.000345	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as guanine nucleotide exchange factor (GEF) for RhoA GTPase. {ECO:0000250}.
• 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)

Intolerance Scores

• loftool: 0.846
• rvis_EVS: 1
• rvis_percentile_EVS: 90.72

Haploinsufficiency Scores

• pHI: 0.0981
• hipred: Y
• hipred_score: 0.533
• ghis: 0.459

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.340

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arhgef19

Zebrafish Information Network

• Gene name: arhgef19
• Affected structure: periderm
• Phenotype tag: abnormal
• Phenotype quality: increased size

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;regulation of actin cytoskeleton organization;regulation of Rho protein signal transduction;wound healing;positive regulation of apoptotic process;positive regulation of GTPase activity;regulation of small GTPase mediated signal transduction;Wnt signaling pathway, planar cell polarity pathway
• Cellular component: cytosol
• Molecular function: guanyl-nucleotide exchange factor activity;Rho guanyl-nucleotide exchange factor activity;GTPase activator activity;protein binding