ARHGEF38

Rho guanine nucleotide exchange factor 38, the group of Dbl family Rho GEFs|BAR and Dbl domain containing

Basic information

Region (hg38): 4:105552619-105708093

Links

ENSG00000236699 ∙ NCBI:54848 ∙ OMIM:619919 ∙ HGNC:25968 ∙ Uniprot:Q9NXL2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autism spectrum disorder (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ARHGEF38 gene.

• Inborn genetic diseases (28 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARHGEF38 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			28			28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	1	0

Variants in ARHGEF38

This is a list of pathogenic ClinVar variants found in the ARHGEF38 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-105552818-A-G		not specified	Uncertain significance (May 26, 2023)
4-105552834-G-T		not specified	Uncertain significance (Dec 14, 2022)
4-105589272-G-T		not specified	Uncertain significance (Jun 05, 2023)
4-105589286-A-T		not specified	Uncertain significance (Sep 13, 2023)
4-105589341-A-C		not specified	Uncertain significance (Aug 12, 2021)
4-105589383-A-G		not specified	Uncertain significance (Nov 08, 2022)
4-105613429-G-A		not specified	Uncertain significance (Dec 03, 2021)
4-105613478-C-T		not specified	Uncertain significance (Feb 12, 2024)
4-105630961-A-G		not specified	Uncertain significance (Jul 06, 2021)
4-105631006-A-G		not specified	Uncertain significance (Aug 30, 2022)
4-105631032-A-G		not specified	Uncertain significance (Mar 20, 2023)
4-105645223-T-C		not specified	Uncertain significance (Feb 07, 2023)
4-105645224-G-A		not specified	Uncertain significance (Jan 19, 2024)
4-105645270-G-A		not specified	Uncertain significance (Jan 09, 2024)
4-105645276-C-T		not specified	Uncertain significance (Jun 22, 2021)
4-105645380-A-C		not specified	Uncertain significance (Feb 26, 2024)
4-105648653-C-T			Likely benign (Jan 01, 2023)
4-105654075-A-G		not specified	Uncertain significance (Aug 10, 2021)
4-105654159-A-G		not specified	Uncertain significance (Jul 05, 2023)
4-105655664-A-T		not specified	Uncertain significance (Mar 08, 2024)
4-105655666-G-A		not specified	Uncertain significance (Jan 23, 2023)
4-105655679-A-G		not specified	Uncertain significance (Feb 02, 2022)
4-105655699-G-A		not specified	Uncertain significance (Jan 23, 2024)
4-105659073-T-A		not specified	Uncertain significance (Oct 17, 2023)
4-105659100-T-C		not specified	Uncertain significance (May 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARHGEF38	protein_coding	protein_coding	ENST00000420470	14	155474

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.14e-9	0.928	125264	2	469	125735	0.00187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.649	338	373	0.906	0.0000186	5137
Missense in Polyphen		106	134.52	0.78798		1855
Synonymous	0.386	135	141	0.959	0.00000722	1398
Loss of Function	1.92	19	30.5	0.624	0.00000136	479

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00260	0.00260
Ashkenazi Jewish	0.0240	0.0232
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.00109	0.00106
Middle Eastern	0.000163	0.000163
South Asian	0.000418	0.000392
Other	0.00372	0.00359

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as a guanine-nucleotide releasing factor. {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)

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.171
• ghis: 0.411

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arhgef38
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Biological process: regulation of Rho protein signal transduction
• Cellular component: cytoplasm
• Molecular function: Rho guanyl-nucleotide exchange factor activity