BANF1
Basic information
Region (hg38): 11:66002228-66004149
Links
Phenotypes
GenCC
Source:
- Nestor-Guillermo progeria syndrome (Strong), mode of inheritance: AR
- Nestor-Guillermo progeria syndrome (Limited), mode of inheritance: AR
- Nestor-Guillermo progeria syndrome (Supportive), mode of inheritance: AR
- Nestor-Guillermo progeria syndrome (Limited), mode of inheritance: Unknown
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Nestor-Guillermo progeria syndrome | AR | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Cardiovascular; Craniofacial; Dermatologic; Musculoskeletal | 21932319; 21549337 |
ClinVar
This is a list of variants' phenotypes submitted to
- Nestor-Guillermo_progeria_syndrome (3 variants)
- not_provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the BANF1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003860.4. 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 | 2 | |||||
missense | 1 | |||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 2 | 0 | 1 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
BANF1 | protein_coding | protein_coding | ENST00000312175 | 2 | 2071 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.652 | 0.325 | 125744 | 0 | 4 | 125748 | 0.0000159 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.43 | 23 | 52.0 | 0.442 | 0.00000324 | 578 |
Missense in Polyphen | 3 | 16.314 | 0.1839 | 222 | ||
Synonymous | -0.713 | 26 | 21.8 | 1.19 | 0.00000145 | 175 |
Loss of Function | 1.71 | 0 | 3.41 | 0.00 | 1.97e-7 | 37 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000289 | 0.0000289 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000264 | 0.0000264 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Plays fundamental roles in nuclear assembly, chromatin organization, gene expression and gonad development. May potently compress chromatin structure and be involved in membrane recruitment and chromatin decondensation during nuclear assembly. Contains 2 non-specific dsDNA-binding sites which may promote DNA cross-bridging. {ECO:0000269|PubMed:12163470}.; FUNCTION: (Microbial infection) In case of poxvirus infection, has an antiviral activity by blocking viral DNA replication. {ECO:0000269|PubMed:18005698}.;
- Disease
- DISEASE: Nestor-Guillermo progeria syndrome (NGPS) [MIM:614008]: An atypical progeroid syndrome characterized by normal development in the first years of life, later followed by the emergence of generalized lipoatrophy, severe osteoporosis, and marked osteolysis. The atrophic facial subcutaneous fat pad and the marked osteolysis of the maxilla and mandible result in a typical pseudosenile facial appearance with micrognathia, prominent subcutaneous venous patterning, a convex nasal ridge, and proptosis. Cognitive development is completely normal. Patients do not have cardiovascular dysfunction, atherosclerosis, or metabolic anomalies. {ECO:0000269|PubMed:21549337}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Disease;HIV Life Cycle;Host Interactions of HIV factors;HIV Infection;Vpr-mediated nuclear import of PICs;2-LTR circle formation;Infectious disease;APOBEC3G mediated resistance to HIV-1 infection;Clearance of Nuclear Envelope Membranes from Chromatin;Nuclear Envelope Breakdown;Mitotic Prophase;Initiation of Nuclear Envelope Reformation;Nuclear Envelope Reassembly;Mitotic Anaphase;Mitotic Metaphase and Anaphase;M Phase;Cell Cycle;Interactions of Vpr with host cellular proteins;Cell Cycle, Mitotic;Integration of viral DNA into host genomic DNA;Autointegration results in viral DNA circles;Integration of provirus;Early Phase of HIV Life Cycle
(Consensus)
Recessive Scores
- pRec
- 0.375
Intolerance Scores
- loftool
- 0.488
- rvis_EVS
- -0.01
- rvis_percentile_EVS
- 52.85
Haploinsufficiency Scores
- pHI
- 0.0840
- hipred
- Y
- hipred_score
- 0.658
- ghis
- 0.638
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.781
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Low | Low | Low |
Primary Immunodeficiency | Low | Low | Low |
Cancer | Low | Low | Low |
Mouse Genome Informatics
- Gene name
- Banf1
- Phenotype
Gene ontology
- Biological process
- mitotic nuclear envelope reassembly;response to virus;DNA integration;negative regulation of viral genome replication;nuclear transport;establishment of integrated proviral latency
- Cellular component
- condensed chromosome;nucleus;nuclear envelope;nucleoplasm;cytoplasm;cytosol
- Molecular function
- DNA binding;protein binding;protein C-terminus binding;enzyme binding;identical protein binding;protein homodimerization activity;protein N-terminus binding;LEM domain binding