AGAP4

ArfGAP with GTPase domain, ankyrin repeat and PH domain 4, the group of ArfGAPs|Ankyrin repeat domain containing|BAR-PH domain containing

Basic information

Region (hg38): 10:45825594-45853875

Previous symbols: [ "CTGLF1", "AGAP8", "CTGLF5" ]

Links

ENSG00000188234 ∙ NCBI:119016 ∙ ∙ HGNC:23459 ∙ Uniprot:Q96P64 ∙ 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 AGAP4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AGAP4 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				1		1
missense			94	3		97
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	94	4	0

Variants in AGAP4

This is a list of pathogenic ClinVar variants found in the AGAP4 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-45825926-T-C		not specified	Uncertain significance (Jan 18, 2023)
10-45825935-A-C		not specified	Uncertain significance (Dec 21, 2023)
10-45825940-T-G		not specified	Uncertain significance (Jul 12, 2022)
10-45825958-A-G		not specified	Uncertain significance (Oct 02, 2023)
10-45826012-G-A		not specified	Uncertain significance (Apr 22, 2024)
10-45826018-C-A		not specified	Uncertain significance (Feb 05, 2024)
10-45826018-C-T		not specified	Uncertain significance (Nov 14, 2024)
10-45826078-C-G		not specified	Uncertain significance (May 24, 2024)
10-45826096-G-A		not specified	Uncertain significance (May 05, 2023)
10-45826112-C-T		not specified	Uncertain significance (Jul 13, 2021)
10-45826132-A-T		not specified	Uncertain significance (Oct 13, 2021)
10-45826141-C-T		not specified	Uncertain significance (Nov 27, 2024)
10-45826142-G-A		not specified	Uncertain significance (Jul 06, 2021)
10-45826177-A-G		not specified	Uncertain significance (Jun 21, 2021)
10-45826180-T-C		not specified	Uncertain significance (Jun 21, 2021)
10-45826198-C-T		not specified	Uncertain significance (Dec 28, 2022)
10-45826207-T-C		not specified	Uncertain significance (Apr 19, 2023)
10-45826219-G-A		not specified	Uncertain significance (Nov 07, 2022)
10-45826238-G-C		not specified	Uncertain significance (Dec 13, 2021)
10-45826248-A-C		not specified	Uncertain significance (Nov 13, 2024)
10-45826255-T-A		not specified	Uncertain significance (Jan 09, 2024)
10-45826259-C-T		not specified	Uncertain significance (Nov 09, 2021)
10-45826267-T-C		not specified	Uncertain significance (Dec 02, 2024)
10-45826273-C-G		not specified	Uncertain significance (Dec 10, 2024)
10-45826274-G-A		not specified	Uncertain significance (Aug 30, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AGAP4	protein_coding	protein_coding	ENST00000448048	7	28282

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0508	64	62.9	1.02	0.00000351	4231
Missense in Polyphen		27	26.831	1.0063		1851
Synonymous	1.15	21	28.8	0.728	0.00000187	1253
Loss of Function

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Putative GTPase-activating protein. {ECO:0000305}.

Haploinsufficiency Scores

• pHI: 0.193
• ghis: 0.523

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0172

Gene Damage Prediction

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

Gene ontology

• Biological process: positive regulation of GTPase activity
• Cellular component: nucleus
• Molecular function: GTPase activator activity;metal ion binding