ARHGAP39

Rho GTPase activating protein 39, the group of Rho GTPase activating proteins

Basic information

Region (hg38): 8:144529178-144685846

Links

ENSG00000147799 ∙ NCBI:80728 ∙ OMIM:615880 ∙ HGNC:29351 ∙ Uniprot:Q9C0H5 ∙ 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 ARHGAP39 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARHGAP39 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	2	3
missense			71	5		76
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	71	6	2

Variants in ARHGAP39

This is a list of pathogenic ClinVar variants found in the ARHGAP39 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-144530511-C-T		not specified	Uncertain significance (Jul 25, 2023)
8-144530588-A-G		not specified	Uncertain significance (Jun 01, 2022)
8-144530712-C-T		not specified	Uncertain significance (Jul 09, 2021)
8-144530724-C-G		not specified	Uncertain significance (May 24, 2023)
8-144530736-C-T		not specified	Uncertain significance (Sep 14, 2023)
8-144530809-C-T		not specified	Uncertain significance (Feb 03, 2022)
8-144532311-C-T		not specified	Uncertain significance (May 10, 2024)
8-144533250-C-T		not specified	Uncertain significance (Jun 11, 2021)
8-144533295-G-A		not specified	Uncertain significance (Nov 22, 2023)
8-144534169-T-C		not specified	Uncertain significance (Jun 26, 2023)
8-144537777-G-C		not specified	Likely benign (Jul 14, 2021)
8-144545316-G-A			Benign (Mar 27, 2018)
8-144545362-C-A		not specified	Uncertain significance (Aug 11, 2022)
8-144545390-C-T		not specified	Uncertain significance (May 03, 2023)
8-144545434-C-G		not specified	Uncertain significance (Jun 27, 2023)
8-144545441-C-T		not specified	Uncertain significance (Sep 22, 2021)
8-144545497-C-T		not specified	Uncertain significance (May 20, 2024)
8-144545558-G-T		not specified	Uncertain significance (Mar 30, 2024)
8-144545566-C-T		not specified	Uncertain significance (Mar 30, 2024)
8-144545573-C-T		not specified	Uncertain significance (Mar 30, 2024)
8-144545671-T-C		not specified	Uncertain significance (Sep 14, 2022)
8-144545740-C-T		not specified	Uncertain significance (Sep 01, 2021)
8-144545753-C-T		not specified	Likely benign (Jun 23, 2023)
8-144545759-T-C		not specified	Uncertain significance (Jan 24, 2024)
8-144545780-C-T		not specified	Uncertain significance (Mar 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARHGAP39	protein_coding	protein_coding	ENST00000377307	11	156632

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00819	0.992	125677	0	64	125741	0.000255

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.52	534	725	0.736	0.0000494	7132
Missense in Polyphen		147	256.22	0.57372		2490
Synonymous	-0.956	360	338	1.07	0.0000259	2223
Loss of Function	4.51	13	46.0	0.282	0.00000213	494

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000867	0.0000867
Ashkenazi Jewish	0.000505	0.000496
East Asian	0.00104	0.00103
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000162	0.000158
Middle Eastern	0.00104	0.00103
South Asian	0.000527	0.000523
Other	0.000169	0.000163

dbNSFP

Source: dbNSFP

• Pathway: Developmental Biology;Signal Transduction;Rho GTPase cycle;Inactivation of CDC42 and RAC1;Signaling by Rho GTPases;Signaling by ROBO receptors;Axon guidance (Consensus)

Intolerance Scores

• rvis_EVS: -1.39
• rvis_percentile_EVS: 4.31

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.563
• ghis: 0.591

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arhgap39

Gene ontology

• Biological process: signal transduction;positive regulation of GTPase activity;regulation of small GTPase mediated signal transduction;postsynapse organization
• Cellular component: nucleus;cytoplasm;cytosol;cytoskeleton;glutamatergic synapse
• Molecular function: GTPase activator activity