ARHGAP19

protein-coding

Rho GTPase activating protein 19, the group of Rho GTPase activating proteins

Gene summary

Members of the ARHGAP family, such as ARHGAP19, encode negative regulators of Rho GTPases (see RHOA; MIM 165390), which are involved in cell migration, proliferation, and differentiation, actin remodeling, and G1 cell cycle progression (Lv et al., 2007 [PubMed 17454002]).[supplied by OMIM, Mar 2008]

MANE transcript

NM_032900.6

Inheritance

—

ClinVar variants

P:4U:68B:2

Top phenotype

Charcot-Marie-Tooth disease, axonal, type 2KK

gnomAD constraint

pLI —, LoF o/e 0.77

Max pathogenic AF

—

Genomic locus

chr10:97,222,173-97,292,673

External References & Databases

Ensembl (ENSG00000213390)

Transcript & Mutation Effects

hg38 • Region Span ~70.5 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 ARHGAP19 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 68

Charcot-Marie-Tooth disease, axonal, type 2KKTotal: 6

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_032900.6. 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						0
missense	2 clinvar		68 clinvar	2 clinvar		72
nonsense						0
start loss						0
frameshift	1 clinvar	1 clinvar				2
splice donor/acceptor (+/-2bp)						0
Total	3	1	68	2	0	74

Highest pathogenic variant AF is 0.000034886776

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 34 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_032900.6	RefSeq	NP_116289.4	12	MANE Select
ENST00000358531.9	Ensembl	ENSP00000351333.4	12	MANE Select
NM_001204300.2	RefSeq	NP_001191229.1	11	Standard
NM_001256423.2	RefSeq	NP_001243352.1	12	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

nucleus
cytoplasm
cytosol
plasma membrane
intracellular membrane-bounded organelle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000358531
Coding exons: 12
Length: 73418
Individuals with no LoFs: 125644
Homozygous LoFs: 1
Heterozygous LoFs: 103
Defined: 125748
p: 0.000414

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.341	257	273	0.942	0.0000146	3243
Missense (PolyPhen)		68	80.724	0.84237		961
Synonymous	1.39	83	101	0.824	0.00000527	943
Loss of Function	1.15	22	28.6	0.768	0.00000170	320

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0.00029	0.00029	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00071	0.00071	rare
Finnish	0.00018	0.00018	rare
European (Non-Finnish)	0.00039	0.00039	rare
South Asian	0.00092	0.00088	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: GTPase activator for the Rho-type GTPases by converting them to an inactive GDP-bound state. {ECO:0000250}.;

Intolerance Scores

LoFtool: 0.913
RVIS EVS: 0.35
RVIS percentile EVS: 74.49

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.610