ARHGAP29

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

Basic information

Region (hg38): 1:94148987-94275068

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 (42 variants)
• not provided (21 variants)
• ARHGAP29-related condition (5 variants)
• Nonsyndromic cleft lip with or without cleft palate (4 variants)
• not specified (2 variants)
• Cleft lip with or without cleft palate (1 variants)
• Isolated 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.

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				6	5	11
missense			50	2	1	53
nonsense	1					1
start loss				1		1
frameshift	1		1			2
inframe indel						0
splice donor/acceptor (+/-2bp)	3	1				4
splice region			2		1	3
non coding					1	1
Total	5	1	51	9	7

Highest pathogenic variant AF is 0.0000263

Variants in ARHGAP29

This is a list of pathogenic ClinVar variants found in the ARHGAP29 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-94173868-C-G		ARHGAP29-related disorder	Likely benign (Nov 08, 2021)
1-94173894-T-C		Inborn genetic diseases	Uncertain significance (Jun 22, 2023)
1-94173896-G-A		ARHGAP29-related disorder	Likely benign (Feb 22, 2021)
1-94173943-T-C		Inborn genetic diseases	Uncertain significance (Aug 04, 2023)
1-94173954-T-C		Inborn genetic diseases	Uncertain significance (Jan 10, 2022)
1-94173967-G-A		Inborn genetic diseases	Uncertain significance (May 26, 2022)
1-94174020-G-T		Inborn genetic diseases	Uncertain significance (Apr 17, 2023)
1-94174068-T-A		Inborn genetic diseases	Uncertain significance (Oct 10, 2023)
1-94174289-A-T		ARHGAP29-related disorder	Benign/Likely benign (Dec 31, 2019)
1-94174310-C-T			Benign (Dec 24, 2018)
1-94174373-A-G		ARHGAP29-related disorder	Benign (Dec 31, 2019)
1-94174420-T-C		Inborn genetic diseases	Uncertain significance (Mar 29, 2022)
1-94174431-T-G		Inborn genetic diseases	Uncertain significance (Sep 29, 2023)
1-94174437-T-C		Inborn genetic diseases	Uncertain significance (May 18, 2022)
1-94174443-C-A		Inborn genetic diseases	Uncertain significance (Jul 12, 2022)
1-94174458-C-A		Inborn genetic diseases	Uncertain significance (Oct 03, 2022)
1-94174474-C-T		not specified	Uncertain significance (Jun 25, 2015)
1-94174645-T-C		Inborn genetic diseases	Uncertain significance (Jun 03, 2022)
1-94174648-T-C		Inborn genetic diseases	Uncertain significance (Jun 06, 2023)
1-94174684-T-C		Inborn genetic diseases	Uncertain significance (Feb 28, 2024)
1-94177604-C-T			Benign/Likely benign (Dec 01, 2023)
1-94177640-C-T			Benign (Dec 31, 2019)
1-94177641-G-A		Inborn genetic diseases	Uncertain significance (Oct 26, 2022)
1-94177653-C-T		ARHGAP29-related disorder	Likely benign (Jul 17, 2023)
1-94177673-T-G		ARHGAP29-related disorder	Likely benign (Oct 28, 2019)

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