Experiment / E7ASSFYN15′ UTR / Translation Efficiency MPRA (MPTA)

HEK293 5′UTR variant translation MPRA

A Massively Parallel Screen of 5′UTR Mutations Identifies Variants Impacting Translation and Protein Production in Neurodevelopmental Disorder Genes

An episomal pooled 5′UTR reporter library containing 1,507 allelic pairs and 32,990 barcoded constructs was transiently transfected into HEK293 cells. Barcode UMI counts from DNA, total RNA, 40S, 80S, polysome, and TRAP-associated fractions were used to estimate allele effects on transcript abundance and translation.

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Processed tables are specific to each experiment. Column names, units, measurements, and table structure are not standardized across the database. Check this experiment’s column definitions and quality-control notes before comparing or combining data.

Organism: Human
Taxonomy ID: NCBITaxon:9606
Biosample: CVCL:0045
Reference genome: Not reported / not applicable
Design focus: Variant-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / Untreated

Episomal plasmid MPRA with a CMV-driven tdTomato reporter and barcode in the 3′UTR; six biological HEK293 replicates. Polysome fractionation resolved 40S, 80S, and polysome-associated RNA, with additional total-RNA, DNA, and eGFP-RPL10a TRAP measurements in the GEO matrix.

Processed data

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Filters apply to this table only. The CSV download contains the complete processed table; filtered rows are available through the API.

Column dictionary · 79 definitions

reporter_context_id: Unique normalized variant/transcript reporter context identifier from the study library.
variant_id: Chromosome and genomic position identifying the tested variant.
transcript_id: Ensembl transcript identifier represented by the context.
gene_id: Ensembl gene identifier from the library annotation.
gene_symbol: HGNC gene symbol from the library annotation.
case_control: Original An et al. variant class: proband case or unaffected sibling control.
chromosome: Chromosome of the patient variant.
position: Variant genomic coordinate as reported in the library annotation.
ref_allele: Reference allele in the variant identifier.
alt_allele: Alternative allele in the variant identifier.
family_id: Family identifier from the source variant collection.
sample_id: Source sample/context identifier from the annotated library.
strand: Annotated transcript strand.
annotation_accession: Transcript accession used for library annotation.
ref_5utr_sequence: Reference synthetic 5′UTR reporter sequence used for this context.
alt_5utr_sequence: Alternative synthetic 5′UTR reporter sequence used for this context.
ref_sequence_length: Length in nucleotides of the reference reporter 5′UTR sequence.
alt_sequence_length: Length in nucleotides of the alternative reporter 5′UTR sequence.
ref_mfe: Predicted minimum free energy for the reference sequence.
alt_mfe: Predicted minimum free energy for the alternative sequence.
delta_mfe: Alternative minus reference minimum free energy as supplied by the annotation.
ref_uorf_count: Number of annotated/predicted upstream open reading frames in the reference sequence.
alt_uorf_count: Number of annotated/predicted upstream open reading frames in the alternative sequence.
uorf_change: Source annotation’s uORF deletion/change indicator.
uaug_context_perturbed: Whether the variant perturbs a uAUG start-codon context.
hek_expression: HEK expression annotation for the represented transcript.
any_hek_expressed: Any-isoform HEK expression annotation.
transcript_brain_expressed: Brain expression annotation for the represented transcript.
any_brain_expressed: Any-isoform brain expression annotation.
sfari_gene_score: SFARI gene score annotation.
sfari_gene_syndromic: SFARI syndromic-gene annotation.
sfari_gene_denovo: SFARI de novo-gene annotation.
barcodes_designed_ref: Number of designed barcodes for the reference allele/context in the oligo library.
barcodes_designed_alt: Number of designed barcodes for the alternative allele/context in the oligo library.
sublibrary: In vivo AAV sublibrary (JD487, JD488, or JD489); blank for the pooled HEK result.
n_measures_with_complete_stats: Number of listed ratiometric comparisons with both an author log2FC and q-value after the study’s QC.
qc_status: Rows retained because they have a complete author-tested result for at least one listed comparison; the author’s barcode/replicate filters were applied upstream.
totalRNA_vs_DNA_log2FC: Author-reported oriented log2 fold change for totalRNA_vs_DNA; positive values favor the numerator named in the label.
totalRNA_vs_DNA_pvalue: Model-based allele-effect p-value for totalRNA_vs_DNA.
totalRNA_vs_DNA_LRT_pvalue: Likelihood-ratio test p-value for the allele effect in totalRNA_vs_DNA.
totalRNA_vs_DNA_tstat: Allele-term test statistic for totalRNA_vs_DNA.
totalRNA_vs_DNA_fdr: Author-reported FDR value for totalRNA_vs_DNA.
totalRNA_vs_DNA_empirical_pvalue: Empirical allele-effect p-value from the author’s 10,000 blank-control null comparisons for totalRNA_vs_DNA.
totalRNA_vs_DNA_qvalue: Author-reported q-value (multiple-testing corrected empirical p-value) for totalRNA_vs_DNA.
fraction40S_vs_totalRNA_log2FC: Author-reported oriented log2 fold change for fraction40S_vs_totalRNA; positive values favor the numerator named in the label.
fraction40S_vs_totalRNA_pvalue: Model-based allele-effect p-value for fraction40S_vs_totalRNA.
fraction40S_vs_totalRNA_LRT_pvalue: Likelihood-ratio test p-value for the allele effect in fraction40S_vs_totalRNA.
fraction40S_vs_totalRNA_tstat: Allele-term test statistic for fraction40S_vs_totalRNA.
fraction40S_vs_totalRNA_fdr: Author-reported FDR value for fraction40S_vs_totalRNA.
fraction40S_vs_totalRNA_empirical_pvalue: Empirical allele-effect p-value from the author’s 10,000 blank-control null comparisons for fraction40S_vs_totalRNA.
fraction40S_vs_totalRNA_qvalue: Author-reported q-value (multiple-testing corrected empirical p-value) for fraction40S_vs_totalRNA.
fraction80S_vs_totalRNA_log2FC: Author-reported oriented log2 fold change for fraction80S_vs_totalRNA; positive values favor the numerator named in the label.
fraction80S_vs_totalRNA_pvalue: Model-based allele-effect p-value for fraction80S_vs_totalRNA.
fraction80S_vs_totalRNA_LRT_pvalue: Likelihood-ratio test p-value for the allele effect in fraction80S_vs_totalRNA.
fraction80S_vs_totalRNA_tstat: Allele-term test statistic for fraction80S_vs_totalRNA.
fraction80S_vs_totalRNA_fdr: Author-reported FDR value for fraction80S_vs_totalRNA.
fraction80S_vs_totalRNA_empirical_pvalue: Empirical allele-effect p-value from the author’s 10,000 blank-control null comparisons for fraction80S_vs_totalRNA.
fraction80S_vs_totalRNA_qvalue: Author-reported q-value (multiple-testing corrected empirical p-value) for fraction80S_vs_totalRNA.
fractionPolysome_vs_totalRNA_log2FC: Author-reported oriented log2 fold change for fractionPolysome_vs_totalRNA; positive values favor the numerator named in the label.
fractionPolysome_vs_totalRNA_pvalue: Model-based allele-effect p-value for fractionPolysome_vs_totalRNA.
fractionPolysome_vs_totalRNA_LRT_pvalue: Likelihood-ratio test p-value for the allele effect in fractionPolysome_vs_totalRNA.
fractionPolysome_vs_totalRNA_tstat: Allele-term test statistic for fractionPolysome_vs_totalRNA.
fractionPolysome_vs_totalRNA_fdr: Author-reported FDR value for fractionPolysome_vs_totalRNA.
fractionPolysome_vs_totalRNA_empirical_pvalue: Empirical allele-effect p-value from the author’s 10,000 blank-control null comparisons for fractionPolysome_vs_totalRNA.
fractionPolysome_vs_totalRNA_qvalue: Author-reported q-value (multiple-testing corrected empirical p-value) for fractionPolysome_vs_totalRNA.
fraction80S_vs_40S_log2FC: Author-reported oriented log2 fold change for fraction80S_vs_40S; positive values favor the numerator named in the label.
fraction80S_vs_40S_pvalue: Model-based allele-effect p-value for fraction80S_vs_40S.
fraction80S_vs_40S_LRT_pvalue: Likelihood-ratio test p-value for the allele effect in fraction80S_vs_40S.
fraction80S_vs_40S_tstat: Allele-term test statistic for fraction80S_vs_40S.
fraction80S_vs_40S_fdr: Author-reported FDR value for fraction80S_vs_40S.
fraction80S_vs_40S_empirical_pvalue: Empirical allele-effect p-value from the author’s 10,000 blank-control null comparisons for fraction80S_vs_40S.
fraction80S_vs_40S_qvalue: Author-reported q-value (multiple-testing corrected empirical p-value) for fraction80S_vs_40S.
fractionPolysome_vs_80S_log2FC: Author-reported oriented log2 fold change for fractionPolysome_vs_80S; positive values favor the numerator named in the label.
fractionPolysome_vs_80S_pvalue: Model-based allele-effect p-value for fractionPolysome_vs_80S.
fractionPolysome_vs_80S_LRT_pvalue: Likelihood-ratio test p-value for the allele effect in fractionPolysome_vs_80S.
fractionPolysome_vs_80S_tstat: Allele-term test statistic for fractionPolysome_vs_80S.
fractionPolysome_vs_80S_fdr: Author-reported FDR value for fractionPolysome_vs_80S.
fractionPolysome_vs_80S_empirical_pvalue: Empirical allele-effect p-value from the author’s 10,000 blank-control null comparisons for fractionPolysome_vs_80S.
fractionPolysome_vs_80S_qvalue: Author-reported q-value (multiple-testing corrected empirical p-value) for fractionPolysome_vs_80S.

Quality control

The study filtered barcode observations with fewer than 20 UMI counts in either fraction of each ratio within a replicate, required at least three biological replicates containing at least three reference and three alternative barcodes, modeled barcode-level log2 ratios with logratio ~ Allele + (1|BC), and calculated empirical p-values from 10,000 blank-control comparisons followed by q-value correction. This package retains the 1,507 contexts with complete author-reported results in at least one comparison; all six HEK comparisons have complete results for these contexts.

Curation notes

The table joins the author’s per-context allelic result CSVs to the annotated library. The result-file names encode raw fraction order; the 40S-v-80S and 80S-v-polysome logFC signs were multiplied by -1 so the exported labels follow the manuscript’s 80S/40S and polysome/80S orientation. q-values and p-values are unchanged. Reference-genome assembly was not explicitly stated in the accessible paper/data files, so it is null.

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