ACAP1

protein-coding

ArfGAP with coiled-coil, ankyrin repeat and PH domains 1, the group of Ankyrin repeat domain containing|BAR-PH domain containing|ArfGAPs

Gene summary

Predicted to enable GTPase activator activity and zinc ion binding activity. Predicted to be involved in protein transport. Located in membrane. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

CENTB1

MANE transcript

NM_014716.4

Inheritance

—

ClinVar variants

U:108B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.26

Max pathogenic AF

—

Genomic locus

chr17:7,336,529-7,351,477

External References & Databases

Ensembl (ENSG00000072818)

Transcript & Mutation Effects

hg38 • Region Span ~14.9 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 ACAP1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 100

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014716.4. 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			105 clinvar	1 clinvar		106
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	108	1	0	109

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 29 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014716.4	RefSeq	NP_055531.1	22	MANE Select
ENST00000158762.8	Ensembl	ENSP00000158762.3	22	MANE Select
ENST00000570457.6	Ensembl	ENSP00000458173.2	6	Standard
ENST00000575425.1	Ensembl	ENSP00000459422.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Endocytosis - Homo sapiens (human)
Nucleotide-binding Oligomerization Domain (NOD) pathway
Arf6 trafficking events
Arf6 signaling events

Biological Process

protein transport
positive regulation of GTPase activity

Molecular Function

GTPase activator activity
protein binding
metal ion binding

Cellular Component

membrane
recycling endosome membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000158762
Coding exons: 22
Length: 14950
Individuals with no LoFs: 125718
Homozygous LoFs: 0
Heterozygous LoFs: 29
Defined: 125747
p: 0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.30	311	448	0.695	0.0000264	4736
Missense (PolyPhen)		73	153.66	0.47508		1655
Synonymous	1.53	147	173	0.852	0.00000970	1522
Loss of Function	4.53	11	43.0	0.256	0.00000227	465

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00012	rare
Latino/Admixed American	0.00023	0.00020	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.00028	0.00028	rare
European (Non-Finnish)	0.00010	0.000097	rare
South Asian	0.000065	0.000065	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: GTPase-activating protein (GAP) for ADP ribosylation factor 6 (ARF6) required for clathrin-dependent export of proteins from recycling endosomes to trans-Golgi network and cell surface. Required for regulated export of ITGB1 from recycling endosomes to the cell surface and ITGB1-dependent cell migration. {ECO:0000269|PubMed:11062263, ECO:0000269|PubMed:16256741, ECO:0000269|PubMed:17398097, ECO:0000269|PubMed:17664335, ECO:0000269|PubMed:22645133}.;

Recessive Scores

pRec: 0.0993

Intolerance Scores

LoFtool: 0.706
RVIS EVS: 0
RVIS percentile EVS: 54.03

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.549

Gene Damage Prediction

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