AGAP6

protein-coding

ArfGAP with GTPase domain, ankyrin repeat and PH domain 6, the group of Ankyrin repeat domain containing|ArfGAPs|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:

CTGLF3

MANE transcript

NM_001077665.3

Inheritance

—

ClinVar variants

U:143B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.91

Max pathogenic AF

—

Genomic locus

chr10:49,982,190-50,011,654

External References & Databases

Ensembl (ENSG00000204149)

Transcript & Mutation Effects

hg38 • Region Span ~29.5 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 AGAP6 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 144

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001077665.3. 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			2 clinvar	1 clinvar		3
missense			140 clinvar	4 clinvar		144
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	143	5	0	148

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 8 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001077665.3	RefSeq	NP_001071133.2	8	MANE Select
ENST00000412531.7	Ensembl	ENSP00000500374.1	8	MANE Select
ENST00000311652.11	Ensembl	ENSP00000309985.8	8	Standard
ENST00000374056.10	Ensembl	ENSP00000363168.6	7	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: ENST00000412531
Coding exons: 8
Length: 22182
Individuals with no LoFs: 114078
Homozygous LoFs: 463
Heterozygous LoFs: 10930
Defined: 125471
p: 0.0465

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.09	382	326	1.17	0.0000184	4474
Missense (PolyPhen)		95	88.613	1.0721		1366
Synonymous	-0.881	136	124	1.10	0.00000732	1311
Loss of Function	0.272	9	9.93	0.907	4.22e-7	128

Population LoF Frequency

Population	CAF	p-value	Status
African	0.19	0.16	notable
Latino/Admixed American	0.020	0.018	notable
Ashkenazi Jewish	0.030	0.028	notable
East Asian	0.020	0.020	notable
Finnish	0.10	0.058	notable
European (Non-Finnish)	0.045	0.043	notable
South Asian	0.050	0.049	notable
Other	0.043	0.041	notable

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: 0.0344

Gene Damage Prediction

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