AGAP4

protein-coding

ArfGAP with GTPase domain, ankyrin repeat and PH domain 4, the group of ArfGAPs|Ankyrin repeat domain containing|BAR-PH domain containing

Gene summary

Predicted to enable GTPase activator activity and GTPase activity. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

CTGLF1
AGAP8
CTGLF5

MANE transcript

NM_001276343.3

Inheritance

—

ClinVar variants

U:147B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e —

Max pathogenic AF

—

Genomic locus

chr10:45,825,594-45,853,875

External References & Databases

Ensembl (ENSG00000188234)

Transcript & Mutation Effects

hg38 • Region Span ~28.3 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 AGAP4 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 151

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001276343.3. 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				1 clinvar		1
missense			147 clinvar	5 clinvar		152
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	147	6	0	153

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001276343.3	RefSeq	NP_001263272.2	8	MANE Select
ENST00000616763.6	Ensembl	ENSP00000483751.2	8	MANE Select
NM_001393377.1	RefSeq	NP_001380306.1	8	Standard
NM_001393378.1	RefSeq	NP_001380307.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

positive regulation of GTPase activity

Molecular Function

GTPase activator activity
metal ion binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000448048
Coding exons: 7
Length: 28282

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0508	64	62.9	1.02	0.00000351	4231
Missense (PolyPhen)		27	26.831	1.0063		1851
Synonymous	1.15	21	28.8	0.728	0.00000187	1253
Loss of Function

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Putative GTPase-activating protein. {ECO:0000305}.;

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0172

Gene Damage Prediction

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