ARHGAP6

Rho GTPase activating protein 6, the group of Rho GTPase activating proteins|MicroRNA protein coding host genes

Basic information

Region (hg38): X:11117650-11665920

Links

ENSG00000047648 ∙ NCBI:395 ∙ OMIM:300118 ∙ HGNC:676 ∙ Uniprot:O43182 ∙ 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 ARHGAP6 gene.

• not provided (59 variants)
• Inborn genetic diseases (32 variants)
• Linear skin defects with multiple congenital anomalies 1 (5 variants)
• X-linked amelogenesis imperfecta hypoplastic/hypomaturation 2 (3 variants)
• not specified (3 variants)
• Amelogenesis imperfecta type 1E (3 variants)
• HCCS-related condition (2 variants)
• Neurodevelopmental disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARHGAP6 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				8	7	15
missense			23	4	2	29
nonsense						0
start loss						0
frameshift						0
inframe indel				1		1
splice donor/acceptor (+/-2bp)				1		1
splice region				1		1
non coding	2	3	13	14	18	50
Total	2	3	36	28	27

Variants in ARHGAP6

This is a list of pathogenic ClinVar variants found in the ARHGAP6 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-11118170-A-G			Benign (Apr 09, 2019)
X-11118490-T-C			Likely benign (Mar 10, 2023)
X-11118538-A-G		HCCS-related disorder	Uncertain significance (Feb 23, 2023)
X-11118547-A-G		Inborn genetic diseases	Conflicting classifications of pathogenicity (Apr 09, 2023)
X-11118560-A-C		HCCS-related disorder	Uncertain significance (Dec 01, 2023)
X-11118573-C-T			Benign (Aug 10, 2023)
X-11118574-G-A		Linear skin defects with multiple congenital anomalies 1	not provided (-)
X-11118588-G-A		HCCS-related disorder	Benign/Likely benign (Mar 31, 2023)
X-11118619-G-T		Linear skin defects with multiple congenital anomalies 1	Uncertain significance (Jul 13, 2023)
X-11118620-C-T		HCCS-related disorder	Conflicting classifications of pathogenicity (May 25, 2022)
X-11118627-A-G		not specified • HCCS-related disorder	Benign/Likely benign (Apr 19, 2023)
X-11120047-T-C			Likely benign (Mar 01, 2023)
X-11120925-A-G			Likely benign (Aug 25, 2022)
X-11120925-A-T			Likely benign (Nov 06, 2023)
X-11120934-C-A			Benign (Feb 01, 2018)
X-11120954-A-G		Inborn genetic diseases	Uncertain significance (Oct 03, 2022)
X-11120974-C-T		Linear skin defects with multiple congenital anomalies 1	Pathogenic (Nov 01, 2006)
X-11120991-G-C			Uncertain significance (Jan 06, 2024)
X-11120998-G-C		Linear skin defects with multiple congenital anomalies 1	Uncertain significance (Jul 22, 2023)
X-11121012-GTGT-G			Benign (Jan 24, 2024)
X-11121593-T-C			Likely benign (Jun 04, 2022)
X-11121636-C-T			Likely benign (Jun 20, 2023)
X-11121641-G-C			Pathogenic (Oct 16, 2022)
X-11121652-C-T		Linear skin defects with multiple congenital anomalies 1 • HCCS-related disorder	Likely pathogenic (Feb 27, 2023)
X-11121657-C-T			Benign/Likely benign (Jan 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARHGAP6	protein_coding	protein_coding	ENST00000337414	13	547583

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.998	0.00155	125742	1	5	125748	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.82	282	382	0.738	0.0000308	6233
Missense in Polyphen		43	98.18	0.43797		1723
Synonymous	0.636	167	178	0.939	0.0000158	2008
Loss of Function	4.52	2	27.7	0.0723	0.00000193	489

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000134	0.0000992
East Asian	0.00	0.00
Finnish	0.0000625	0.0000462
European (Non-Finnish)	0.0000511	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: GTPase activator for the Rho-type GTPases by converting them to an inactive GDP-bound state. Could regulate the interactions of signaling molecules with the actin cytoskeleton. Promotes continuous elongation of cytoplasmic processes during cell motility and simultaneous retraction of the cell body changing the cell morphology. {ECO:0000269|PubMed:10699171}.
• Pathway: Signal Transduction;rho cell motility signaling pathway;t cell receptor signaling pathway;rac1 cell motility signaling pathway;Rho GTPase cycle;adp-ribosylation factor;Signaling by Rho GTPases;Regulation of RhoA activity (Consensus)

Recessive Scores

• pRec: 0.140

Intolerance Scores

• loftool: 0.326
• rvis_EVS: -0.56
• rvis_percentile_EVS: 19.73

Haploinsufficiency Scores

• pHI: 0.202
• hipred: Y
• hipred_score: 0.783
• ghis: 0.522

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.123

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arhgap6
• Phenotype: growth/size/body region 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); embryo phenotype; normal phenotype

Gene ontology

• Biological process: Rho protein signal transduction;positive regulation of signal transduction;actin filament polymerization;positive regulation of GTPase activity;focal adhesion assembly;regulation of small GTPase mediated signal transduction;negative regulation of stress fiber assembly;negative regulation of focal adhesion assembly
• Cellular component: cytoplasm;cytosol;actin filament;actin cytoskeleton
• Molecular function: SH3/SH2 adaptor activity;GTPase activator activity;SH3 domain binding