ARHGAP29

Rho GTPase activating protein 29, the group of AH/BAR family Rho GTPase activating proteins

Basic information

Region (hg38): 1:94148988-94275068

Links

ENSG00000137962 ∙ NCBI:9411 ∙ OMIM:610496 ∙ HGNC:30207 ∙ Uniprot:Q52LW3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• cleft lip with or without cleft palate (Definitive), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ARHGAP29 gene.

• Inborn_genetic_diseases (123 variants)
• not_provided (35 variants)
• ARHGAP29-related_disorder (27 variants)
• Nonsyndromic_cleft_lip_with_or_without_cleft_palate (4 variants)
• not_specified (2 variants)
• Isolated_cleft_palate (1 variants)
• Cleft_palate (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARHGAP29 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000004815.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				13	5	18
missense			138	7	2	147
nonsense	2		1			3
start loss				1		1
frameshift		1	1			2
splice donor/acceptor (+/-2bp)	3	1				4
Total	5	2	140	21	7

Highest pathogenic variant AF is 0.0000161123

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARHGAP29	protein_coding	protein_coding	ENST00000260526	22	126081

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000356	125716	0	31	125747	0.000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.21	559	646	0.866	0.0000325	8323
Missense in Polyphen		169	250.48	0.6747		3382
Synonymous	0.758	206	220	0.935	0.0000108	2345
Loss of Function	6.09	8	58.1	0.138	0.00000317	748

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000231	0.000231
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000218	0.000217
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000107	0.000105
Middle Eastern	0.000218	0.000217
South Asian	0.0000327	0.0000327
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: GTPase activator for the Rho-type GTPases by converting them to an inactive GDP-bound state. Has strong activity toward RHOA, and weaker activity toward RAC1 and CDC42. May act as a specific effector of RAP2A to regulate Rho. In concert with RASIP1, suppresses RhoA signaling and dampens ROCK and MYH9 activities in endothelial cells and plays an essential role in blood vessel tubulogenesis. {ECO:0000269|PubMed:15752761, ECO:0000269|PubMed:9305890}.
• Pathway: Hypothetical Craniofacial Development Pathway;Signal Transduction;Rho GTPase cycle;Signaling by Rho GTPases (Consensus)

Recessive Scores

• pRec: 0.0887

Intolerance Scores

• loftool: 0.481
• rvis_EVS: -1.48
• rvis_percentile_EVS: 3.69

Haploinsufficiency Scores

• pHI: 0.0876
• hipred: Y
• hipred_score: 0.742
• ghis: 0.581

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.431

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arhgap29
• Phenotype: digestive/alimentary phenotype; embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); craniofacial phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: Rho protein signal transduction;positive regulation of GTPase activity;regulation of small GTPase mediated signal transduction
• Cellular component: cytoplasm;cytosol;protein-containing complex
• Molecular function: GTPase activator activity;PDZ domain binding;metal ion binding