AGAP9

ArfGAP with GTPase domain, ankyrin repeat and PH domain 9, the group of BAR-PH domain containing|Ankyrin repeat domain containing|ArfGAPs

Basic information

Region (hg38): 10:47501854-47523638

Previous symbols: [ "CTGLF6" ]

Links

ENSG00000204172 ∙ NCBI:642517 ∙ ∙ HGNC:23463 ∙ Uniprot:Q5VTM2 ∙ 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 AGAP9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AGAP9 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			1	1		2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	1	1	0

Variants in AGAP9

This is a list of pathogenic ClinVar variants found in the AGAP9 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-47503383-C-A		not specified	Uncertain significance (Jun 18, 2021)
10-47503387-T-C			Likely benign (Dec 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AGAP9	protein_coding	protein_coding	ENST00000413193	8	47895

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.359	0.493	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.183	4	5.17	0.774	2.17e-7	4636
Missense in Polyphen		0	0	NaN		485
Synonymous	0.205	1	1.30	0.771	5.50e-8	1371
Loss of Function	0.777	0	0.704	0.00	2.95e-8	151

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
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
• ghis: 0.420

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene ontology

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