AGFG1

ArfGAP with FG repeats 1, the group of ArfGAPs|MicroRNA protein coding host genes

Basic information

Region (hg38): 2:227472151-227561217

Previous symbols: [ "HRB" ]

Links

ENSG00000173744 ∙ NCBI:3267 ∙ OMIM:600862 ∙ HGNC:5175 ∙ Uniprot:P52594 ∙ 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 AGFG1 gene.

• Inborn genetic diseases (15 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AGFG1 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				3		3
missense			13	2		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1	1		2
Total	0	0	14	6	0

Variants in AGFG1

This is a list of pathogenic ClinVar variants found in the AGFG1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-227472492-C-T		not specified	Uncertain significance (Nov 06, 2023)
2-227520027-A-G		not specified	Uncertain significance (Sep 14, 2023)
2-227520032-T-A		not specified	Uncertain significance (Oct 22, 2021)
2-227523801-T-C			Likely benign (Feb 01, 2023)
2-227523863-C-A		not specified	Uncertain significance (Jan 16, 2024)
2-227524850-C-T		not specified	Uncertain significance (Oct 06, 2021)
2-227524852-C-T		not specified	Uncertain significance (Jan 23, 2023)
2-227524865-C-T		not specified	Uncertain significance (Jul 12, 2023)
2-227531118-C-T		not specified	Uncertain significance (Nov 22, 2021)
2-227531186-T-A		not specified	Uncertain significance (Jul 14, 2022)
2-227532165-G-A		not specified	Uncertain significance (Oct 12, 2022)
2-227532168-T-C			Likely benign (Jul 04, 2018)
2-227533680-A-G		not specified	Likely benign (Feb 01, 2023)
2-227533738-A-G		not specified	Uncertain significance (Feb 07, 2023)
2-227533741-T-C		not specified	Uncertain significance (Dec 13, 2023)
2-227534870-G-A			Likely benign (Jul 17, 2018)
2-227534883-G-C		not specified	Uncertain significance (Mar 29, 2022)
2-227534999-G-A			Likely benign (Jul 01, 2022)
2-227536638-A-C		not specified	Uncertain significance (Oct 26, 2022)
2-227536666-C-T		not specified	Uncertain significance (Jun 16, 2023)
2-227536696-C-T		not specified	Uncertain significance (Mar 22, 2023)
2-227536954-T-C		not specified	Uncertain significance (Aug 22, 2023)
2-227552113-C-T			Likely benign (Nov 01, 2022)
2-227554478-A-G		not specified	Uncertain significance (Dec 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AGFG1	protein_coding	protein_coding	ENST00000409979	14	89063

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.993	0.00724	125729	0	5	125734	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.66	225	307	0.733	0.0000143	3814
Missense in Polyphen		54	108.08	0.49962		1429
Synonymous	-0.347	116	111	1.04	0.00000558	1169
Loss of Function	4.37	3	27.9	0.107	0.00000128	325

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000868	0.0000868
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000265	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for vesicle docking or fusion during acrosome biogenesis (By similarity). May play a role in RNA trafficking or localization. In case of infection by HIV-1, acts as a cofactor for viral Rev and promotes movement of Rev-responsive element- containing RNAs from the nuclear periphery to the cytoplasm. This step is essential for HIV-1 replication. {ECO:0000250, ECO:0000269|PubMed:10613896, ECO:0000269|PubMed:14701878, ECO:0000269|PubMed:15749819}.
• Pathway: Influenza A - Homo sapiens (human);Vesicle-mediated transport;Membrane Trafficking;Clathrin-mediated endocytosis;Cargo recognition for clathrin-mediated endocytosis (Consensus)

Recessive Scores

• pRec: 0.222

Intolerance Scores

• loftool: 0.589
• rvis_EVS: -0.36
• rvis_percentile_EVS: 28.93

Haploinsufficiency Scores

• pHI: 0.163
• hipred: Y
• hipred_score: 0.654
• ghis: 0.642

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.986

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Agfg1
• Phenotype: reproductive system phenotype; cellular phenotype

Gene ontology

• Biological process: acrosome assembly;mRNA export from nucleus;multicellular organism development;spermatid nucleus differentiation;positive regulation of GTPase activity;intermediate filament organization;membrane organization
• Cellular component: nuclear pore;cytosol;cytoplasmic vesicle;cell projection;neuronal cell body;intracellular membrane-bounded organelle
• Molecular function: DNA binding;RNA binding;GTPase activator activity;protein binding;metal ion binding