ARHGEF39

Rho guanine nucleotide exchange factor 39, the group of Dbl family Rho GEFs

Basic information

Region (hg38): 9:35658874-35675866

Previous symbols: [ "C9orf100" ]

Links

ENSG00000137135 ∙ NCBI:84904 ∙ ∙ HGNC:25909 ∙ Uniprot:Q8N4T4 ∙ 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 ARHGEF39 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARHGEF39 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						0
missense			22	2		24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			22	2	2	26
Total	0	0	44	4	2

Variants in ARHGEF39

This is a list of pathogenic ClinVar variants found in the ARHGEF39 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-35660573-G-C		not specified	Uncertain significance (Feb 28, 2023)
9-35660580-C-G		not specified	Uncertain significance (Nov 18, 2022)
9-35660590-C-G		not specified	Uncertain significance (Sep 15, 2021)
9-35660643-G-A		not specified	Uncertain significance (Aug 14, 2023)
9-35660646-C-T		not specified	Uncertain significance (Jul 14, 2021)
9-35660753-A-G		not specified	Uncertain significance (Jun 16, 2023)
9-35660756-C-G		not specified	Uncertain significance (Jan 03, 2024)
9-35660801-A-G		not specified	Uncertain significance (Apr 17, 2024)
9-35660823-G-T		not specified	Uncertain significance (Apr 22, 2024)
9-35660826-A-G		not specified	Uncertain significance (Dec 06, 2022)
9-35660838-A-C		not specified	Uncertain significance (Nov 08, 2021)
9-35660842-G-A		not specified	Uncertain significance (Aug 04, 2023)
9-35660843-G-A		not specified	Uncertain significance (Jul 25, 2023)
9-35660855-C-T		not specified	Uncertain significance (Mar 01, 2023)
9-35660868-C-T		not specified	Likely benign (Sep 14, 2022)
9-35660952-C-G		not specified	Uncertain significance (May 15, 2024)
9-35661009-C-T		not specified	Uncertain significance (Jan 03, 2024)
9-35661084-G-A		not specified	Uncertain significance (Apr 09, 2024)
9-35661125-A-T		not specified	Uncertain significance (Mar 07, 2023)
9-35661172-A-T		not specified	Uncertain significance (Aug 21, 2023)
9-35661946-A-C			Benign (Jan 18, 2019)
9-35662183-T-C		not specified	Uncertain significance (Jun 22, 2023)
9-35662248-T-A		not specified	Uncertain significance (May 17, 2023)
9-35662603-G-A		not specified	Uncertain significance (Mar 23, 2023)
9-35662618-A-T		not specified	Uncertain significance (Dec 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARHGEF39	protein_coding	protein_coding	ENST00000378387	9	16992

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.13e-10	0.174	125686	0	62	125748	0.000247

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.569	173	195	0.885	0.0000116	2118
Missense in Polyphen		62	75.689	0.81914		871
Synonymous	0.698	66	73.6	0.897	0.00000344	696
Loss of Function	0.612	17	19.9	0.852	0.00000108	205

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000425	0.000423
Ashkenazi Jewish	0.00	0.00
East Asian	0.000164	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000365	0.000352
Middle Eastern	0.000164	0.000163
South Asian	0.000294	0.000294
Other	0.000166	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Promotes cell proliferation. {ECO:0000269|PubMed:22327280}.
• 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: 0.0879

Intolerance Scores

• rvis_EVS: 0.86
• rvis_percentile_EVS: 88.69

Haploinsufficiency Scores

• pHI: 0.0980
• hipred: N
• hipred_score: 0.197
• ghis: 0.471

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arhgef39

Gene ontology

• Biological process: positive regulation of cell migration;regulation of Rho protein signal transduction
• Cellular component: plasma membrane
• Molecular function: Rho guanyl-nucleotide exchange factor activity;protein binding