AGFG1
Basic information
Region (hg38): 2:227472152-227561217
Previous symbols: [ "HRB" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (43 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. These statistics are base on transcript: NM_000004504.5. 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 | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 3 | |||||
| missense | 40 | 43 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 40 | 6 | 0 |
GnomAD
Source:
| 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:
- 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