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

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 ClinVar and linked to the BANF1 gene.

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.

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			1		1	2
missense						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			12	4	10	26
Total	0	0	13	4	11

Variants in BANF1

This is a list of pathogenic ClinVar variants found in the BANF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-66002233-G-A		Nestor-Guillermo progeria syndrome	Likely benign (Jan 12, 2018)
11-66002276-G-T		Nestor-Guillermo progeria syndrome	Likely benign (Apr 27, 2017)
11-66002300-C-T		Nestor-Guillermo progeria syndrome	Uncertain significance (Jan 13, 2018)
11-66002309-T-G		Nestor-Guillermo progeria syndrome	Benign (Jan 12, 2018)
11-66002338-G-C		Nestor-Guillermo progeria syndrome	Benign (Jan 12, 2018)
11-66002425-G-A		Nestor-Guillermo progeria syndrome	Uncertain significance (Jan 12, 2018)
11-66002444-G-A		Nestor-Guillermo progeria syndrome	Uncertain significance (Jan 12, 2018)
11-66002495-A-T		Nestor-Guillermo progeria syndrome	Uncertain significance (Jan 13, 2018)
11-66002517-T-G		Nestor-Guillermo progeria syndrome	Uncertain significance (Jan 12, 2018)
11-66002525-A-G		Nestor-Guillermo progeria syndrome	Uncertain significance (Jan 13, 2018)
11-66002527-C-T		Nestor-Guillermo progeria syndrome	Uncertain significance (Jan 15, 2018)
11-66002932-T-C			Benign (Jun 19, 2021)
11-66002942-G-A			Benign (Jun 18, 2021)
11-66003074-G-A			Benign (Nov 10, 2018)
11-66003187-A-G			Benign (Nov 10, 2018)
11-66003259-C-T		Nestor-Guillermo progeria syndrome	Uncertain significance (Jan 13, 2018)
11-66003284-G-A		Nestor-Guillermo progeria syndrome	Pathogenic (May 13, 2011)
11-66003482-G-A			Benign (Nov 10, 2018)
11-66003579-TCACTGAG-T			Benign (Nov 10, 2018)
11-66003706-C-T		Nestor-Guillermo progeria syndrome	Benign (Dec 31, 2019)
11-66003836-T-A		Nestor-Guillermo progeria syndrome	Uncertain significance (Jan 13, 2018)
11-66003872-C-T		Nestor-Guillermo progeria syndrome	Likely benign (Apr 28, 2017)
11-66003892-T-A		Nestor-Guillermo progeria syndrome	Uncertain significance (Jan 13, 2018)
11-66003900-C-A		Nestor-Guillermo progeria syndrome	Benign (Jan 13, 2018)
11-66003915-T-A		Nestor-Guillermo progeria syndrome	Uncertain significance (Jan 12, 2018)

GnomAD

Source: gnomAD

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: 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_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

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