ARHGAP11A

protein-coding

Rho GTPase activating protein 11A, the group of Rho GTPase activating proteins

Gene summary

This gene encodes a member of the Rho GTPase activating protein family. In response to DNA damage, the encoded protein interacts with the p53 tumor suppressor protein and stimulates its tetramerization, which results in cell-cycle arrest and apoptosis. A chromosomal deletion that includes this gene is one cause of Prader-Willi syndrome, and an intronic variant of this gene may be associated with sleep duration in children. This gene is highly expressed in colon cancers and in a human basal-like breast cancer cell line. This gene also produces a ARHGAP11A-SCG5 readthrough transcript and ARHGAP11A-SCG5 protein. [provided by RefSeq, Feb 2019]

MANE transcript

NM_014783.6

Inheritance

—

ClinVar variants

P:1U:137B:18

Top phenotype

Inborn genetic diseases

gnomAD constraint

pLI —, LoF o/e 0.52

Max pathogenic AF

—

Genomic locus

chr15:32,615,144-32,639,941

External References & Databases

Ensembl (ENSG00000198826)

Transcript & Mutation Effects

hg38 • Region Span ~24.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ARHGAP11A variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 133

not providedTotal: 10

Inborn genetic diseasesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014783.6. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			4 clinvar	2 clinvar	5 clinvar	11
missense			127 clinvar	9 clinvar	2 clinvar	138
nonsense			3 clinvar			3
start loss						0
frameshift		1 clinvar				1
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	1	137	11	7	156

Highest pathogenic variant AF is 0.00036986603

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 25 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014783.6	RefSeq	NP_055598.1	12	MANE Select
ENST00000361627.8	Ensembl	ENSP00000355090.3	12	MANE Select
NM_001286479.3	RefSeq	NP_001273408.1	8	Standard
NM_001286480.3	RefSeq	NP_001273409.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Signal Transduction
Rho GTPase cycle
Signaling by Rho GTPases

Biological Process

signal transduction
positive regulation of GTPase activity
regulation of small GTPase mediated signal transduction

Molecular Function

GTPase activator activity

Cellular Component

cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000361627
Coding exons: 12
Length: 24806
Individuals with no LoFs: 125544
Homozygous LoFs: 1
Heterozygous LoFs: 203
Defined: 125748
p: 0.000811

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.00549	522	522	0.999	0.0000254	6697
Missense (PolyPhen)		88	113.02	0.77862		1479
Synonymous	0.270	183	188	0.975	0.00000940	1960
Loss of Function	2.87	21	40.7	0.515	0.00000212	569

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00099	0.00098	rare
Latino/Admixed American	0.00029	0.00029	rare
Ashkenazi Jewish	0.00011	0.000099	rare
East Asian	0.00082	0.00082	rare
Finnish	0.0027	0.0027	notable
European (Non-Finnish)	0.00063	0.00062	rare
South Asian	0.00095	0.00095	rare
Other	0.00066	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0806

Intolerance Scores

LoFtool: 0.426
RVIS EVS: -0.21
RVIS percentile EVS: 37.74

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.750

Gene Damage Prediction

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