AGAP5

ArfGAP with GTPase domain, ankyrin repeat and PH domain 5, the group of BAR-PH domain containing|ArfGAPs|Ankyrin repeat domain containing

Basic information

Region (hg38): 10:73674286-73698109

Previous symbols: [ "CTGLF2" ]

Links

ENSG00000172650 ∙ NCBI:729092 ∙ ∙ HGNC:23467 ∙ Uniprot:A6NIR3 ∙ 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 AGAP5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AGAP5 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						0
missense			39	1		40
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	39	1	0

Variants in AGAP5

This is a list of pathogenic ClinVar variants found in the AGAP5 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-73674639-T-G		not specified	Uncertain significance (Nov 01, 2022)
10-73674657-G-A		not specified	Uncertain significance (Aug 13, 2021)
10-73674666-C-T		not specified	Uncertain significance (Jan 05, 2022)
10-73674670-C-T		not specified	Uncertain significance (Jan 05, 2022)
10-73674675-G-T		not specified	Uncertain significance (May 27, 2022)
10-73674681-G-C		not specified	Uncertain significance (Dec 16, 2023)
10-73674791-G-C		not specified	Uncertain significance (Aug 08, 2022)
10-73674874-C-T		not specified	Uncertain significance (Jul 09, 2021)
10-73674957-C-T		not specified	Uncertain significance (Dec 01, 2022)
10-73674958-G-A		not specified	Uncertain significance (Dec 01, 2022)
10-73674967-G-A		not specified	Uncertain significance (Feb 17, 2024)
10-73675008-T-C		not specified	Uncertain significance (Feb 13, 2024)
10-73675021-T-G		not specified	Uncertain significance (Jun 17, 2024)
10-73675035-C-G		not specified	Uncertain significance (Dec 08, 2023)
10-73675084-C-A		not specified	Uncertain significance (Jun 04, 2024)
10-73675135-G-C		not specified	Uncertain significance (Apr 24, 2024)
10-73675137-C-G		not specified	Uncertain significance (Feb 07, 2023)
10-73675239-C-T		not specified	Uncertain significance (May 13, 2024)
10-73675315-A-G		not specified	Uncertain significance (Jul 12, 2022)
10-73675323-A-G		not specified	Uncertain significance (Oct 06, 2021)
10-73675458-T-G		not specified	Uncertain significance (Jan 31, 2024)
10-73675462-T-G		not specified	Uncertain significance (Nov 29, 2021)
10-73675528-T-A		not specified	Uncertain significance (Apr 06, 2022)
10-73675543-C-T		not specified	Uncertain significance (Mar 07, 2023)
10-73675581-C-T		not specified	Uncertain significance (Mar 19, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AGAP5	protein_coding	protein_coding	ENST00000374094	8	23607

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00592	0.746	124768	0	5	124773	0.0000200

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.543	185	207	0.894	0.0000119	4389
Missense in Polyphen		44	63.869	0.68891		1550
Synonymous	-0.308	84	80.5	1.04	0.00000505	1292
Loss of Function	0.835	4	6.25	0.640	2.67e-7	125

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000869	0.0000869
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.0814

Essentials

• essential_gene_CRISPR: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0389

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