AGAP3

ArfGAP with GTPase domain, ankyrin repeat and PH domain 3, the group of Ankyrin repeat domain containing|ArfGAPs|BAR-PH domain containing

Basic information

Region (hg38): 7:151085831-151144436

Previous symbols: [ "CENTG3" ]

Links

ENSG00000133612 ∙ NCBI:116988 ∙ OMIM:616813 ∙ HGNC:16923 ∙ Uniprot:Q96P47 ∙ 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 AGAP3 gene.

• not_specified (104 variants)
• not_provided (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AGAP3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000031946.7. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2	1	3
missense			99	4	1	104
nonsense						0
start loss						0
frameshift			1		1	2
splice donor/acceptor (+/-2bp)						0
Total	0	0	100	6	3

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AGAP3	protein_coding	protein_coding	ENST00000397238	18	58606

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.911	0.0891	124782	0	20	124802	0.0000801

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.99	377	580	0.650	0.0000394	5845
Missense in Polyphen		120	250.13	0.47975		2386
Synonymous	-0.460	265	256	1.04	0.0000180	1941
Loss of Function	4.95	8	43.0	0.186	0.00000232	450

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000392	0.000375
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000489	0.0000464
European (Non-Finnish)	0.0000722	0.0000706
Middle Eastern	0.00	0.00
South Asian	0.0000655	0.0000654
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: GTPase-activating protein for the ADP ribosylation factor family (Potential). GTPase which may be involved in the degradation of expanded polyglutamine proteins through the ubiquitin-proteasome pathway. {ECO:0000269|PubMed:16461359, ECO:0000305}.
• Pathway: Endocytosis - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.221
• rvis_EVS: -1
• rvis_percentile_EVS: 8.54

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.685
• ghis: 0.654

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.331

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Agap3

Gene ontology

• Biological process: obsolete protein import into nucleus, translocation;signal transduction;cellular response to reactive oxygen species;proteasome-mediated ubiquitin-dependent protein catabolic process;positive regulation of GTPase activity
• Cellular component: nucleus;cytoplasm;membrane;cell periphery
• Molecular function: GTPase activity;GTPase activator activity;GTP binding;polyubiquitin modification-dependent protein binding;metal ion binding