GeneBe

BANF1

BAF nuclear assembly factor 1

Basic information

Region (hg38): 11:66002228-66004149

Links

ENSG00000175334 ∙ NCBI:8815 ∙ OMIM:603811 ∙ HGNC:17397 ∙ Uniprot:O75531 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • 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: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Nestor-Guillermo progeria syndromeARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingCardiovascular; Craniofacial; Dermatologic; Musculoskeletal21932319; 21549337

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BANF1 gene.

  • 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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
1
clinvar
 2
missense
1
clinvar
 1
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 2 0 1
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
BANF1protein_codingprotein_codingENST00000312175 22071
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.6520.325125744041257480.0000159
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.432352.00.4420.00000324578
Missense in Polyphen316.3140.1839222
Synonymous-0.7132621.81.190.00000145175
Loss of Function1.7103.410.001.97e-737

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00002890.0000289
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00002640.0000264
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianLowLowLow
Primary ImmunodeficiencyLowLowLow
CancerLowLowLow

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