BPHunter

BPHunter

Genome-wide detection of human variants that disrupt intronic branchpoints

Pre-mRNA splicing, as a necessary step for protein-coding gene expression in eukaryotic cells, operates spliceosome mostly within introns to define the exon-intron boundaries and hence the coding sequences.
 
Intronic branchpoint (BP) is recognized by the spliceosome in the beginning of splicing, and constitutes a vulnerability of splicing by its potential variants. BP variants may potentially result in aberrant splicing (exon skipping, intron retention), which could be deleterious to gene produdcts.
 
BPHunter is a genome-wide approach to systematically detect intronic variants that may disrupt BP recognition, efficiently and informatively.
 
Reference: Zhang P. et al. Genome-wide detection of human variants that disrupt intronic branchpoints. PNAS. 2022. [PMID:36306325] [Paper]

Upload Variants (human GRCh38 genome assembly):

Upload your variants in VCF format, with only the first 5 tab-delimited columns: CHR, POS, ID, REF, ALT.
Limit your dataset < 1,000,000 variants, which typically requires ~7 seconds of processing time.
You can download a sample dataset here.



Transcripts:
Canonical(based on MANE)
All (based on GENCODE)


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Developer| Peng ZHANG   Ph.D.

Lab Head | Jean-Laurent CASANOVA   M.D., Ph.D.

Laboratory | Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University

Last Update| June 23, 2025

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The Rockefeller University, New York, USA

BPHunter is developed and maintained by: Peng ZHANG