AGAP2

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

Basic information

Region (hg38): 12:57723761-57742157

Previous symbols: [ "CENTG1" ]

Links

ENSG00000135439

∙ NCBI:116986 ∙ OMIM:605476 ∙ HGNC:16921 ∙ Uniprot:Q99490 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the AGAP2 gene.

not_specified (117 variants)
AGAP2-related_disorder (14 variants)
not_provided (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AGAP2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001122772.3. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	9 clinvar	1 clinvar	11
missense			120 clinvar	4 clinvar	1 clinvar	125
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	121	13	2

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AGAP2	protein_coding	protein_coding	ENST00000547588	19	16961

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.998	0.00184	125741	0	7	125748	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.39	401	643	0.624	0.0000369	7467
Missense in Polyphen		129	257.51	0.50096		2807
Synonymous	1.04	252	274	0.920	0.0000158	2642
Loss of Function	5.58	7	49.3	0.142	0.00000292	520

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.000206	0.000198
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: GTPase-activating protein (GAP) for ARF1 and ARF5, which also shows strong GTPase activity. Isoform 1 participates in the prevention of neuronal apoptosis by enhancing PI3 kinase activity. It aids the coupling of metabotropic glutamate receptor 1 (GRM1) to cytoplasmic PI3 kinase by interacting with Homer scaffolding proteins, and also seems to mediate anti-apoptotic effects of NGF by activating nuclear PI3 kinase. Isoform 2 does not stimulate PI3 kinase but may protect cells from apoptosis by stimulating Akt. It also regulates the adapter protein 1 (AP-1)-dependent trafficking of proteins in the endosomal system. It seems to be oncogenic. It is overexpressed in cancer cells, prevents apoptosis and promotes cancer cell invasion. {ECO:0000269|PubMed:12640130, ECO:0000269|PubMed:14761976, ECO:0000269|PubMed:15118108, ECO:0000269|PubMed:16079295}.;
Pathway: Endocytosis - Homo sapiens (human);FoxO signaling pathway - Homo sapiens (human);Prolactin Signaling Pathway;JAK-STAT;Developmental Biology;Netrin-1 signaling;Axon guidance;Netrin-mediated signaling events;Trk receptor signaling mediated by PI3K and PLC-gamma (Consensus)

Recessive Scores

pRec: 0.233

Intolerance Scores

loftool: 0.494
rvis_EVS: -0.18
rvis_percentile_EVS: 40.56

Haploinsufficiency Scores

pHI: 0.817
hipred: Y
hipred_score: 0.669
ghis: 0.599

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: S
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.530

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Agap2
Phenotype: liver/biliary system phenotype; homeostasis/metabolism phenotype; cellular phenotype; endocrine/exocrine gland phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan);

Gene ontology

Biological process: protein transport;negative regulation of protein catabolic process;negative regulation of neuron apoptotic process;positive regulation of GTPase activity;positive regulation of 1-phosphatidylinositol-3-kinase activity
Cellular component: nucleus;nucleolus;cytoplasm;mitochondrion;membrane;extracellular exosome
Molecular function: GTPase activity;GTPase activator activity;protein binding;GTP binding;metal ion binding