ACAP3

protein-coding

ArfGAP with coiled-coil, ankyrin repeat and PH domains 3, the group of ArfGAPs|BAR-PH domain containing|Ankyrin repeat domain containing|MicroRNA protein coding host genes

Gene summary

Predicted to enable GTPase activator activity and zinc ion binding activity. Predicted to act upstream of or within neuron migration and regulation of neuron projection development. Predicted to be located in endosome membrane and growth cone. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

CENTB5

MANE transcript

NM_030649.3

Inheritance

—

ClinVar variants

U:155B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.39

Max pathogenic AF

—

Genomic locus

chr1:1,292,390-1,309,609

External References & Databases

Ensembl (ENSG00000131584)

Transcript & Mutation Effects

hg38 • Region Span ~17.2 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 ACAP3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 140

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_030649.3. 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			4 clinvar	2 clinvar		6
missense			144 clinvar	2 clinvar		146
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			7 clinvar			7
Total	0	0	155	4	0	159

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 58 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_030649.3	RefSeq	NP_085152.2	24	MANE Select
ENST00000354700.10	Ensembl	ENSP00000346733.5	24	MANE Select
ENST00000353662.4	Ensembl	ENSP00000321139.4	21	Standard
ENST00000354980.7	Ensembl	ENSP00000347075.2	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Endocytosis - Homo sapiens (human)

Biological Process

neuron migration
regulation of neuron projection development
positive regulation of GTPase activity

Molecular Function

GTPase activator activity
metal ion binding

Cellular Component

growth cone

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000354700
Coding exons: 24
Length: 17234
Individuals with no LoFs: 125118
Homozygous LoFs: 0
Heterozygous LoFs: 22
Defined: 125140
p: 0.0000879

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.67	410	517	0.793	0.0000365	5353
Missense (PolyPhen)		70	130.97	0.53448		1391
Synonymous	-1.40	254	227	1.12	0.0000177	1608
Loss of Function	3.73	17	43.5	0.390	0.00000201	512

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000063	0.000062	rare
Latino/Admixed American	0.000031	0.000029	rare
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.00018	0.00016	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00011	0.00011	rare
South Asian	0.000070	0.000065	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: GTPase-activating protein for the ADP ribosylation factor family. {ECO:0000305}.;

Recessive Scores

pRec: 0.110

Intolerance Scores

LoFtool: 0.471
RVIS EVS: -0.35
RVIS percentile EVS: 29.49

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.781

Gene Damage Prediction

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