AGFG1

protein-coding

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

Gene summary

The protein encoded by this gene is related to nucleoporins, a class of proteins that mediate nucleocytoplasmic transport. The encoded protein binds the activation domain of the human immunodeficiency virus Rev protein when Rev is assembled onto its RNA target, and is required for the nuclear export of Rev-directed RNAs. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2008]

Previous symbols:

MANE transcript

NM_004504.5

Inheritance

—

ClinVar variants

U:58B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.11

Max pathogenic AF

—

Genomic locus

chr2:227,472,152-227,561,217

External References & Databases

Ensembl (ENSG00000173744)

Transcript & Mutation Effects

hg38 • Region Span ~89.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to AGFG1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 49

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_004504.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	3 clinvar		5
missense			47 clinvar	3 clinvar		50
nonsense			1 clinvar			1
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	58	6	0	64

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 53 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_004504.5	RefSeq	NP_004495.2	13	MANE Select
ENST00000310078.13	Ensembl	ENSP00000312059.7	13	MANE Select
NM_001135187.2	RefSeq	NP_001128659.1	14	Standard
NM_001135188.2	RefSeq	NP_001128660.1	13	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Influenza A - Homo sapiens (human)
Vesicle-mediated transport
Membrane Trafficking
Clathrin-mediated endocytosis
Cargo recognition for clathrin-mediated endocytosis

Biological Process

acrosome assembly
mRNA export from nucleus
multicellular organism development
spermatid nucleus differentiation
positive regulation of GTPase activity

Molecular Function

DNA binding
RNA binding
GTPase activator activity
protein binding
metal ion binding

Cellular Component

nuclear pore
cytosol
cytoplasmic vesicle
cell projection
neuronal cell body

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000409979
Coding exons: 14
Length: 89063
Individuals with no LoFs: 125729
Homozygous LoFs: 0
Heterozygous LoFs: 5
Defined: 125734
p: 0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.66	225	307	0.733	0.0000143	3814
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000026	0.000018	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.222

Intolerance Scores

LoFtool: 0.589
RVIS EVS: -0.36
RVIS percentile EVS: 28.93

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.986

Gene Damage Prediction

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