AGAP9

protein-coding

ArfGAP with GTPase domain, ankyrin repeat and PH domain 9, the group of BAR-PH domain containing|Ankyrin repeat domain containing|ArfGAPs

Gene summary

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

Previous symbols:

CTGLF6

MANE transcript

NM_001190810.1

Inheritance

—

ClinVar variants

U:1B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr10:47,501,854-47,523,638

External References & Databases

Ensembl (ENSG00000204172)

Transcript & Mutation Effects

hg38 • Region Span ~21.8 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 AGAP9 variants in ClinVar

2 Conditions Cataloged

not providedTotal: 1

not specifiedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001190810.1. 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			1 clinvar	1 clinvar		2
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	1	1	0	2

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 3 of 3 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001190810.1	RefSeq	NP_001177739.1	8	MANE Select
ENST00000452145.6	Ensembl	ENSP00000392206.2	8	MANE Select
ENST00000975180.1	Ensembl	ENSP00000644997.1	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: ENST00000413193
Coding exons: 8
Length: 47895
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.183	4	5.17	0.774	2.17e-7	4636
Missense (PolyPhen)		0	0	NaN		485
Synonymous	0.205	1	1.30	0.771	5.50e-8	1371
Loss of Function	0.777	0	0.704	0.00	2.95e-8	151

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: 0.114