BNC2

Chr 9AD

basonuclin zinc finger protein 2

Also known as: BSN2, LUTO, bn2

NCBI Gene: 54796ENSG00000173068UniProt: Q6ZN30OMIM: 608669

BNC2 encodes a zinc finger transcription factor that regulates keratinocyte differentiation and plays an important role in early urinary tract development. Mutations cause congenital lower urinary tract obstruction with autosomal dominant inheritance. The gene is highly constrained against loss-of-function variants (pLI 0.93, LOEUF 0.34), indicating that complete loss of function is likely incompatible with normal development.

OMIMResearchSummary from RefSeq, OMIM, UniProt
LOFmechanismADLOEUF 0.341 OMIM phenotype
Clinical Summary— BNC2
⚡
Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 0.93). One damaged copy is likely sufficient to cause disease.
📋
ClinVar Variants
101 unique Pathogenic / Likely Pathogenic· 230 VUS of 459 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
LoF intolerant — likely haploinsufficient
LoF Constraint
0.34LOEUF
pLI 0.928
Z-score 4.53
OE 0.17 (0.09–0.34)
Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint
0.36Z-score
OE missense 0.96 (0.90–1.03)
584 obs / 609.0 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.17 (0.09–0.34)
0≤0.351.4
Missense OE0.96 (0.90–1.03)
0≤0.61.4
Synonymous OE1.14
0≤1.21.6
LoF obs/exp: 6 / 34.8Missense obs/exp: 584 / 609.0Syn Z: -1.64
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
definitiveBNC2-related congenital lower urinary tract obstructionLOFAD
DN
0.3495th %ile
GOF
0.2796th %ile
LOF
0.82top 5%

The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).

LOFprediction above median · 1 literature citation · LOEUF 0.34

Literature Evidence

LOFThese human developmental defects may be the consequence of bnc2 haploinsufficiency caused by disruption of the gene.PMID:19706529

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.

ClinVar Variant Classifications

459 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic95
Likely Pathogenic6
VUS230
Likely Benign69
Benign28
Conflicting9
95
Pathogenic
6
Likely Pathogenic
230
VUS
69
Likely Benign
28
Benign
9
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
1
1
93
0
95
Likely Pathogenic
0
0
6
0
6
VUS
4
206
19
1
230
Likely Benign
0
11
12
46
69
Benign
0
10
5
13
28
Conflicting
—9
Total522813560437

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

BNC2 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Genetic variant of BNC2 gene is functionally associated with adolescent idiopathic scoliosis in Chinese population.
Xu L et al.·Mol Genet Genomics
2017Functional
Rare Variants in BNC2 Are Implicated in Autosomal-Dominant Congenital Lower Urinary-Tract Obstruction.
Kolvenbach CM et al.·Am J Hum Genet
2019
Association between genetic polymorphisms and risk of adolescent idiopathic scoliosis in case-control studies: a systematic review.
Terhune E et al.·J Med Genet
2024Review
Overexpression of Basonuclin Zinc Finger Protein 2 in stromal cell is related to mesenchymal phenotype and immunosuppression of mucinous colorectal adenocarcinoma.
Yin QZ et al.·Int Immunopharmacol
2024
Development of a CAFs-related gene signature to predict survival and drug response in bladder cancer.
Zhang Z et al.·Hum Cell
2022
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients