ADAP2

protein-coding

ArfGAP with dual PH domains 2, the group of Pleckstrin homology domain containing|ArfGAPs

Gene summary

The protein encoded by this gene binds beta-tubulin and increases the stability of microtubules. The encoded protein can also translocate to the cell membrane and bind phosphatidylinositol 3,4,5-trisphosphate (PtdInsP3) and inositol 1,3,4,5-tetrakisphosphate (InsP4). In addition, this protein is a GTPase-activating protein for ADP ribosylation factor 6 and may be able to block the entry of some RNA viruses. [provided by RefSeq, Oct 2016]

Previous symbols:

CENTA2

MANE transcript

NM_018404.3

Inheritance

—

ClinVar variants

U:55B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.73

Max pathogenic AF

—

Genomic locus

chr17:30,906,344-30,959,945

External References & Databases

Ensembl (ENSG00000184060)

Transcript & Mutation Effects

hg38 • Region Span ~53.6 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 ADAP2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 53

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018404.3. 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						0
missense			51 clinvar	2 clinvar		53
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	55	2	0	57

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 54 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018404.3	RefSeq	NP_060874.1	11	MANE Select
ENST00000330889.8	Ensembl	ENSP00000329468.3	11	MANE Select
NM_001346712.2	RefSeq	NP_001333641.1	11	Standard
NM_001346714.2	RefSeq	NP_001333643.1	11	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
adap2	Danio rerio	Structure: atrioventricular valve Quality: morphology abnormal

Gene / Model

Organism

Observed Phenotype

adap2

Danio rerio

Structure: atrioventricular valve

Quality: morphology

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

TYROBP Causal Network

Biological Process

heart development
positive regulation of GTPase activity

Molecular Function

GTPase activator activity
protein binding
phosphatidylinositol-4,5-bisphosphate binding
phosphatidylinositol-3,4,5-trisphosphate binding
protein binding, bridging

Cellular Component

cytoplasm
mitochondrial envelope
plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000330889
Coding exons: 11
Length: 52979
Individuals with no LoFs: 125567
Homozygous LoFs: 2
Heterozygous LoFs: 179
Defined: 125748
p: 0.000720

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.803	172	204	0.842	0.0000116	2496
Missense (PolyPhen)		66	88.782	0.74339		1131
Synonymous	0.832	66	75.2	0.878	0.00000397	715
Loss of Function	1.26	18	24.8	0.727	0.00000137	263

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00043	0.00043	rare
Latino/Admixed American	0.00023	0.00023	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00016	rare
Finnish	0.00097	0.00092	rare
European (Non-Finnish)	0.0012	0.0012	notable
South Asian	0.00020	0.00020	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: GTPase-activating protein for the ADP ribosylation factor family (Potential). Binds phosphatidylinositol 3,4,5- trisphosphate (PtdInsP3) and inositol 1,3,4,5-tetrakisphosphate (InsP4). Possesses a stoichiometry of two binding sites for InsP4 with identical affinity. {ECO:0000269|PubMed:14690521, ECO:0000305}.;

Recessive Scores

pRec: 0.116

Intolerance Scores

LoFtool: 0.739
RVIS EVS: -0.45
RVIS percentile EVS: 24

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.512

Gene Damage Prediction

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