ACAP2

protein-coding

ArfGAP with coiled-coil, ankyrin repeat and PH domains 2, the group of ArfGAPs|BAR-PH domain containing|Ankyrin repeat domain containing

Gene summary

Enables GTPase activator activity. Acts upstream of or within actin filament-based process. Located in plasma membrane and ruffle. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

CENTB2

MANE transcript

NM_012287.6

Inheritance

—

ClinVar variants

U:51B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.19

Max pathogenic AF

—

Genomic locus

chr3:195,274,745-195,443,044

External References & Databases

Ensembl (ENSG00000114331)

Transcript & Mutation Effects

hg38 • Region Span ~168.3 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 ACAP2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 45

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_012287.6. 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			2 clinvar	1 clinvar		3
missense			46 clinvar			46
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	51	1	0	52

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 56 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_012287.6	RefSeq	NP_036419.3	23	MANE Select
ENST00000326793.11	Ensembl	ENSP00000324287.6	23	MANE Select
ENST00000439666.1	Ensembl	ENSP00000411336.1	2	Standard
ENST00000439758.3	Ensembl	ENSP00000413388.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Endocytosis - Homo sapiens (human)
Arf6 signaling events

Biological Process

endocytic recycling
positive regulation of GTPase activity
cellular response to nerve growth factor stimulus

Molecular Function

GTPase activator activity
Rab GTPase binding
metal ion binding
phosphatidylinositol-3,5-bisphosphate binding

Cellular Component

endosome membrane
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000326793
Coding exons: 23
Length: 168343
Individuals with no LoFs: 125734
Homozygous LoFs: 0
Heterozygous LoFs: 12
Defined: 125746
p: 0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	3.22	224	407	0.551	0.0000208	5133
Missense (PolyPhen)		48	118.8	0.40404		1419
Synonymous	1.55	121	145	0.836	0.00000767	1373
Loss of Function	5.42	10	52.3	0.191	0.00000300	619

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
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)	0.000080	0.000079	rare
South Asian	0	0.0	absent
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: GTPase-activating protein (GAP) for ADP ribosylation factor 6 (ARF6). {ECO:0000269|PubMed:11062263}.;

Recessive Scores

pRec: 0.115

Intolerance Scores

LoFtool: 0.487
RVIS EVS: -0.6
RVIS percentile EVS: 17.91

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.719

Gene Damage Prediction

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