AGAP6

ArfGAP with GTPase domain, ankyrin repeat and PH domain 6, the group of Ankyrin repeat domain containing|ArfGAPs|BAR-PH domain containing

Basic information

Region (hg38): 10:49982189-50011654

Previous symbols: [ "CTGLF3" ]

Links

ENSG00000204149 ∙ NCBI:414189 ∙ ∙ HGNC:23466 ∙ Uniprot:Q5VW22 ∙ 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 AGAP6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AGAP6 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			57	2		59
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	57	3	1

Variants in AGAP6

This is a list of pathogenic ClinVar variants found in the AGAP6 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-49988738-G-A		not specified	Uncertain significance (May 16, 2024)
10-49988752-G-A		not specified	Uncertain significance (Nov 22, 2023)
10-49988818-G-A		not specified	Uncertain significance (Feb 22, 2023)
10-49988842-G-T		not specified	Uncertain significance (Mar 18, 2024)
10-49988849-T-C		not specified	Uncertain significance (Jun 18, 2024)
10-49988862-A-G			Likely benign (May 01, 2022)
10-49988935-G-C		not specified	Uncertain significance (Jan 31, 2024)
10-49991696-G-A		not specified	Uncertain significance (Mar 20, 2023)
10-50002009-G-A		not specified	Likely benign (Aug 11, 2022)
10-50002030-T-C		not specified	Likely benign (Sep 20, 2023)
10-50008771-T-A		not specified	Uncertain significance (Dec 08, 2023)
10-50008774-T-C		not specified	Uncertain significance (Mar 01, 2023)
10-50008802-A-G		not specified	Uncertain significance (Dec 20, 2023)
10-50008831-A-G		not specified	Uncertain significance (May 27, 2022)
10-50008847-C-T		not specified	Uncertain significance (Jun 09, 2022)
10-50008862-G-A		not specified	Uncertain significance (May 16, 2023)
10-50008914-C-A		not specified	Uncertain significance (Dec 14, 2021)
10-50008914-CAA-C			Benign (Apr 02, 2018)
10-50008954-G-A		not specified	Uncertain significance (Oct 16, 2023)
10-50008963-A-G		not specified	Uncertain significance (Feb 16, 2023)
10-50009000-G-A		not specified	Uncertain significance (Jun 27, 2022)
10-50009023-T-A		not specified	Uncertain significance (Jun 03, 2022)
10-50009038-G-C		not specified	Uncertain significance (Nov 18, 2022)
10-50009095-A-G		not specified	Uncertain significance (Jan 09, 2024)
10-50009123-T-A		not specified	Uncertain significance (Dec 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AGAP6	protein_coding	protein_coding	ENST00000412531	8	22182

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000259	0.315	114078	463	10930	125471	0.0465

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.09	382	326	1.17	0.0000184	4474
Missense in Polyphen		95	88.613	1.0721		1366
Synonymous	-0.881	136	124	1.10	0.00000732	1311
Loss of Function	0.272	9	9.93	0.907	4.22e-7	128

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.210	0.183
Ashkenazi Jewish	0.0299	0.0280
East Asian	0.0200	0.0198
Finnish	0.102	0.0579
European (Non-Finnish)	0.0445	0.0430
Middle Eastern	0.0200	0.0198
South Asian	0.0501	0.0488
Other	0.0434	0.0414

dbNSFP

Source: dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.115
• ghis: 0.547

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0344

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