BANF1

Chr 11AR

barrier to autointegration nuclear assembly factor 1

Also known as: BAF, BCRP1, D14S1460, NGPS

NCBI Gene: 8815 ENSG00000175334 UniProt: O75531 OMIM: 603811

The BANF1 protein is a non-specific DNA-binding protein essential for nuclear membrane reformation during cell division, chromatin organization, and regulation of innate immune responses to foreign DNA. Autosomal recessive mutations cause Nestor-Guillermo progeria syndrome, a rare premature aging disorder. This gene has a GeneReviews entry available for detailed clinical information.

GeneReviews OMIM ResearchSummary from RefSeq, OMIM, UniProt

The protein encoded by this gene was first identified by its ability to protect retroviruses from intramolecular integration and therefore promote intermolecular integration into the host cell genome. The protein forms a homodimer which localizes to both the nucleus and cytoplasm and is specifically associated with chromosomes during mitosis. This protein binds to double stranded DNA in a non-specific manner and also binds to LEM-domain containing proteins of the nuclear envelope. This protein is thought to facilitate nuclear reassembly by binding with both DNA and inner nuclear membrane proteins and thereby recruit chromatin to the nuclear periphery. Alternative splicing results in multiple transcript variants encoding the same protein.[provided by RefSeq, Jan 2009]

GeneReviews OMIM ResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

Nestor-Guillermo progeria syndromeMIM #614008

Clinical highlights

Gene–disease validity (ClinGen)

Limited · Nestor-Guillermo progeria syndrome · AR · ClinGen 2024

not for standalone diagnostic reporting

Interpreting a novel variant

Loss of function is the curated mechanism (Gene2Phenotype) and the gene is intolerant of it in the population — truncating, frameshift and canonical splice variants carry more prior weight here than missense.Curated gene-level mechanism — a prior for triage, not a per-variant call.

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.87

LOEUF

LOF

Mechanism· G2P

📖

GeneReview available — BANF1

Authoritative clinical overview · Recommended first read

Open GeneReview ↗

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Moderate LoF intolerance

LoF Constraint?

0.87LOEUF

pLI 0.652

Z-score 1.71

OE 0.00 (0.00–0.87)

Moderately constrained

Typical tolerance to LoF variation

Missense Constraint?

1.43Z-score

OE missense 0.44 (0.32–0.63)

23 obs / 52.0 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.00 (0.00–0.87)

0≤0.351.4

Missense OE?0.44 (0.32–0.63)

0≤0.61.4

Synonymous OE?1.19

0≤1.21.6

LoF obs/exp: 0 / 3.4Missense obs/exp: 23 / 52.0Syn Z: -0.71

Background carrier burden — how many people carry a rare variant somewhere in BANF1?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 2,400

50 rare PASS variants

Rare truncating (LoF)

1 in 120,000

4 rare PASS variants

Rare synonymous (reference)

1 in 880

50 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for BANF1. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 7 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 3,000	≈ 1 in 140,000
South Asian	~43k	1 in 1,700	none seen
Remaining (unassigned)	~30k	1 in 3,000	none seen
European (Finnish)	~27k	≈ 1 in 8,900	≈ 1 in 27,000
Admixed American	~22k	1 in 3,700	none seen
African / African American	~21k	1 in 2,000	≈ 1 in 17,000
East Asian	~20k	1 in 1,700	none seen

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): All 2 coding exons well covered in gnomAD exomes and genomes.? see exons ↓