AGFG2

ArfGAP with FG repeats 2, the group of ArfGAPs

Basic information

Region (hg38): 7:100539203-100568220

Previous symbols: [ "HRBL" ]

Links

ENSG00000106351 ∙ NCBI:3268 ∙ OMIM:604019 ∙ HGNC:5177 ∙ Uniprot:O95081 ∙ 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 AGFG2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AGFG2 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			25	2		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	2	0

Variants in AGFG2

This is a list of pathogenic ClinVar variants found in the AGFG2 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-100539443-G-A		not specified	Uncertain significance (May 12, 2024)
7-100539498-C-T		not specified	Uncertain significance (Oct 10, 2023)
7-100548869-C-T		not specified	Uncertain significance (Dec 07, 2023)
7-100548902-C-A		not specified	Uncertain significance (Mar 20, 2023)
7-100550462-C-G		not specified	Uncertain significance (Sep 20, 2023)
7-100553354-C-T		not specified	Uncertain significance (Jun 11, 2021)
7-100553358-C-T		not specified	Uncertain significance (Oct 10, 2023)
7-100554114-C-T		not specified	Uncertain significance (Apr 08, 2024)
7-100554118-C-T		not specified	Uncertain significance (May 13, 2022)
7-100554168-G-C		not specified	Uncertain significance (Feb 09, 2023)
7-100554228-C-A		not specified	Uncertain significance (Mar 28, 2022)
7-100555616-C-T		not specified	Uncertain significance (May 23, 2023)
7-100555686-C-G		not specified	Uncertain significance (Dec 18, 2023)
7-100562268-A-T		not specified	Uncertain significance (Feb 07, 2023)
7-100562274-C-T		not specified	Uncertain significance (Nov 08, 2022)
7-100562330-G-A		not specified	Likely benign (Oct 05, 2022)
7-100562354-G-A		not specified	Uncertain significance (Nov 03, 2023)
7-100562632-C-G		not specified	Uncertain significance (Dec 06, 2022)
7-100562638-C-T		not specified	Uncertain significance (Apr 07, 2022)
7-100562646-G-A		not specified	Likely benign (Dec 14, 2023)
7-100562646-G-T		not specified	Uncertain significance (May 26, 2024)
7-100562652-G-A		not specified	Uncertain significance (Mar 13, 2023)
7-100562664-A-G		not specified	Uncertain significance (Jun 29, 2023)
7-100562679-G-C		not specified	Uncertain significance (Dec 28, 2023)
7-100562941-C-T		not specified	Uncertain significance (Feb 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AGFG2	protein_coding	protein_coding	ENST00000300176	12	29009

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000254	0.985	125684	0	64	125748	0.000255

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.890	222	263	0.845	0.0000145	3074
Missense in Polyphen		37	59.255	0.62442		806
Synonymous	0.710	100	109	0.914	0.00000678	1038
Loss of Function	2.15	9	19.1	0.470	8.18e-7	233

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000149	0.000149
Ashkenazi Jewish	0.00	0.00
East Asian	0.00136	0.00136
Finnish	0.0000999	0.0000924
European (Non-Finnish)	0.000195	0.000193
Middle Eastern	0.00136	0.00136
South Asian	0.000262	0.000261
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.666
• rvis_EVS: 0.95
• rvis_percentile_EVS: 90.06

Haploinsufficiency Scores

• pHI: 0.152
• hipred: Y
• hipred_score: 0.504
• ghis: 0.442

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.916

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Agfg2

Gene ontology

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