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): 10:49982190-50011654

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.

• not_specified (127 variants)
• not_provided (1 variants)

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. These statistics are base on transcript: NM_001077665.3. 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				1		1
missense			123	4		127
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	123	5	0

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