AGAP1

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

Basic information

Region (hg38): 2:235494042-236131793

Previous symbols: [ "CENTG2" ]

Links

ENSG00000157985 ∙ NCBI:116987 ∙ OMIM:608651 ∙ HGNC:16922 ∙ Uniprot:Q9UPQ3 ∙ 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 AGAP1 gene.

• not provided (150 variants)
• Inborn genetic diseases (31 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AGAP1 gene is commonly pathogenic or not.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				33	17	50
missense			81	3	3	87
nonsense						0
start loss						0
frameshift			1		1	2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			2	7	2	11
non coding				18	6	24
Total	0	0	82	54	27

Variants in AGAP1

This is a list of pathogenic ClinVar variants found in the AGAP1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
2-235494699-C-G			Uncertain significance (Jun 27, 2022)
2-235494710-C-A			Likely benign (Apr 30, 2022)
2-235494722-C-T			Likely benign (Jul 20, 2023)
2-235494726-C-T			Uncertain significance (Jul 06, 2022)
2-235494727-G-A			Uncertain significance (Jul 09, 2022)
2-235494762-A-G			Uncertain significance (Mar 01, 2022)
2-235494793-G-A		not specified	Uncertain significance (May 23, 2023)
2-235494795-G-T		not specified	Uncertain significance (Jan 04, 2024)
2-235494818-C-T			Benign (Jan 29, 2024)
2-235494840-G-T			Uncertain significance (Mar 12, 2023)
2-235494842-C-T			Likely benign (Jan 24, 2023)
2-235494853-A-T			Uncertain significance (Jun 29, 2023)
2-235494861-G-C			Likely benign (Mar 12, 2022)
2-235494867-T-C			Benign (Nov 23, 2023)
2-235709160-G-C			Likely benign (Feb 09, 2023)
2-235709162-GTCC-G			Likely benign (Jul 02, 2022)
2-235709165-C-T			Likely benign (Feb 20, 2022)
2-235709168-C-G			Likely benign (Jun 27, 2022)
2-235709180-T-C			Likely benign (Oct 19, 2022)
2-235709184-T-A			Uncertain significance (Jun 12, 2023)
2-235709186-C-T			Likely benign (Oct 30, 2023)
2-235709191-A-G			Uncertain significance (Jun 23, 2023)
2-235709218-C-T		not specified	Uncertain significance (Apr 12, 2022)
2-235709224-C-T			Uncertain significance (Oct 15, 2023)
2-235709225-G-A			Benign (Jan 22, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AGAP1	protein_coding	protein_coding	ENST00000304032	18	637712

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000162	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.29	481	567	0.848	0.0000377	5588
Missense in Polyphen		219	264.65	0.82752		2833
Synonymous	-1.64	283	250	1.13	0.0000190	1723
Loss of Function	5.86	6	51.3	0.117	0.00000313	480

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000531	0.0000527
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 for ARF1 and, to a lesser extent, ARF5. Directly and specifically regulates the adapter protein 3 (AP-3)-dependent trafficking of proteins in the endosomal-lysosomal system. {ECO:0000269|PubMed:12640130}.
• Pathway: Endocytosis - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.315
• rvis_EVS: -2.39
• rvis_percentile_EVS: 1.1

Haploinsufficiency Scores

• pHI: 0.855
• hipred: Y
• hipred_score: 0.675
• ghis: 0.600

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.365

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Agap1
• Phenotype: vision/eye phenotype; skeleton phenotype; immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); craniofacial phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: protein transport;positive regulation of GTPase activity
• Cellular component: nucleus;cytoplasm
• Molecular function: GTPase activity;GTPase activator activity;GTP binding;phospholipid binding;metal ion binding