AGAP5

protein-coding

ArfGAP with GTPase domain, ankyrin repeat and PH domain 5, the group of BAR-PH domain containing|ArfGAPs|Ankyrin repeat domain containing

Gene summary

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

Previous symbols:

CTGLF2

MANE transcript

NM_001144000.4

Inheritance

—

ClinVar variants

U:126B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.64

Max pathogenic AF

—

Genomic locus

chr10:73,674,287-73,698,109

External References & Databases

Ensembl (ENSG00000172650)

Transcript & Mutation Effects

hg38 • Region Span ~23.8 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 AGAP5 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 124

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001144000.4. 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			124 clinvar	1 clinvar		125
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	126	1	0	127

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 6 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001144000.4	RefSeq	NP_001137472.1	8	MANE Select
ENST00000374094.9	Ensembl	ENSP00000363207.4	8	MANE Select
ENST00000443782.6	Ensembl	ENSP00000402792.2	7	Standard
ENST00000443782.7	Ensembl	ENSP00000402792.2	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: ENST00000374094
Coding exons: 8
Length: 23607
Individuals with no LoFs: 124768
Homozygous LoFs: 0
Heterozygous LoFs: 5
Defined: 124773
p: 0.0000200

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.543	185	207	0.894	0.0000119	4389
Missense (PolyPhen)		44	63.869	0.68891		1550
Synonymous	-0.308	84	80.5	1.04	0.00000505	1292
Loss of Function	0.835	4	6.25	0.640	2.67e-7	125

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000018	0.000018	rare
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
Indispensability pred.: N
Indispensability score: 0.0389

Gene Damage Prediction

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