COMT protein abundance flow-cytometry MAVE
Integrated multiplexed assays of variant effect reveal determinants of catechol-O-methyltransferase gene expressionA codon-saturation COMT library covering MB-COMT codons 40–74 and 136–158 was stably integrated into the HEK293T landing-pad cell line. Four biological replicates were sorted by flow cytometry and profiled by amplicon sequencing; this table reports the published ALDEx2 effects for the low-protein flow population P3 relative to total genomic DNA.
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.
Perturbation & assay details
Doxycycline induction (2 µg/mL for 21 h) after AP1903 selection; fresh-media stimulation for 1 h 15 min before flow cytometry
This is a targeted genomic-integration saturation-mutagenesis reporter assay rather than a barcode-based episomal MPRA. Bxb1 recombinase inserted the pDEST_HC_Rec_Bxb_v2_UTR5_Flag_COMT_moxGFP_LPS construct into a landing pad, with moxGFP reporting protein abundance and IRES-mCherry serving as a transcript/induction control; all silent and missense substitutions and amber nonsense substitutions were designed across two COMT coding ROIs. The selected flow readout is population P3 relative to total gDNA; population P4 was excluded in the source analysis. MAVEdb defines positive protein-abundance scores as lower protein abundance. Variant effects are published ALDEx2 standardized differences with 75% confidence intervals and FDR.
Processed data
50 rows per page. Click a cell to inspect its full value.
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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 · 38 definitions
- mavedb_accession
- MAVEdb score-set accession and variant row identifier
- hgvs_nt
- Target-relative nucleotide HGVS from MAVEdb
- hgvs_pro_mavedb
- Target-relative protein HGVS from MAVEdb; the target begins at MB-COMT Glu40
- variant_id
- Unique plasmid-reference variant identifier from Dataset EV3
- roi
- Mutagenesis region: ROI_1 is codons 40–74 and ROI_2 is codons 136–158
- position_plasmid
- 1-based plasmid reference coordinate of the first altered base
- ref_nt
- Reference nucleotide or multi-nucleotide sequence
- alt_nt
- Alternate nucleotide or multi-nucleotide sequence
- ref_codon
- Reference codon
- alt_codon
- Alternate codon
- aa_position
- MB-COMT amino-acid position after the N-terminal tag adjustment
- ref_aa
- Reference amino acid in one-letter code
- alt_aa
- Alternate amino acid in one-letter code; * denotes stop
- aa_change
- MB-COMT protein consequence, for example p.E40K
- variant_type
- Silent, Missense, or Nonsense consequence
- mutation_type
- SNP, di_nt_MNP, or tri_nt_MNP substitution class
- polysome_fraction
- NA because this is the protein-abundance experiment
- effect_score
- Author Dataset EV3 full-precision ALDEx2 standardized effect for flow P3 versus total gDNA; cross-checked to the MAVEdb score set
- effect_ci_lower
- Author Dataset EV3 75% ALDEx2 effect confidence-interval lower bound
- effect_ci_higher
- Author Dataset EV3 75% ALDEx2 effect confidence-interval upper bound
- effect_fdr
- Author Dataset EV3 ALDEx2 false-discovery rate
- significant_fdr_0_05
- True when effect_fdr is less than 0.05; this flag was not used to remove rows
- effect_direction
- Direction of the selected score; positive means lower protein abundance
- rsid
- dbSNP or gnomAD rs identifier when present in Dataset EV2
- gnomad_allele_frequency
- gnomAD v3.1.2 allele frequency when present
- transcript
- Transcript identifier from Dataset EV2
- transcript_consequence
- Transcript HGVS consequence from Dataset EV2
- genomic_chromosome
- GRCh38 chromosome from Dataset EV2
- genomic_position
- GRCh38 genomic position from Dataset EV2
- clinvar_clinical_significance
- ClinVar clinical-significance annotation from Dataset EV2
- integrated_rna_effect
- Dataset EV3 RNA-versus-gDNA ALDEx2 effect retained as cross-layer context
- integrated_rna_fdr
- Dataset EV3 RNA-versus-gDNA FDR
- integrated_mid_polysome_effect
- Dataset EV3 F3-versus-RNA ALDEx2 effect retained as cross-layer context
- integrated_mid_polysome_fdr
- Dataset EV3 F3-versus-RNA FDR
- integrated_heavy_polysome_effect
- Dataset EV3 F4-versus-RNA ALDEx2 effect retained as cross-layer context
- integrated_heavy_polysome_fdr
- Dataset EV3 F4-versus-RNA FDR
- integrated_protein_effect
- Dataset EV3 P3-versus-gDNA protein-abundance effect; positive means lower protein abundance
- integrated_protein_fdr
- Dataset EV3 protein-abundance effect FDR
Quality control
The authors called variants with satmut_utils v1.0.3-dev001, retained variants in the two mutagenesis ROIs, required amber UAG/TAG for nonsense calls, required log10 variant frequency greater than -5.8, and removed SNPs with false-positive random-forest predictions in more than half of the gDNA libraries. Variant frequencies were normalized to wild type with a 0.5 pseudocount, negative-control variants were subtracted, batches were ComBat-corrected, and technical replicates were summarized by the median. Only variants observed in all biological replicates and with median natural-log frequency greater than -10 were used for differential comparisons; low-yield/depth polysome fractions 1/2 and flow population 4 were excluded. ALDEx2 used four biological replicates. Package QC retained all 3050 published MAVEdb score rows with finite score and FDR values in the published score set; non-significant variants were retained, and unavailable source annotations are represented as NA.
Curation notes
The biological material is the HEK293T LLP iCasp9 Blast derivative; CVCL:0063 is the Cellosaurus identifier for the parent HEK293T line. MAVEdb HGVS coordinates are target-relative, so c.1 and p.1 correspond to the first assayed MB-COMT codon, Glu40; plasmid coordinates and variant_id preserve the author reference. The two ROIs are separated coding intervals on GRCh38 chr22. Cross-layer Dataset EV3 annotations and Dataset EV2 genomic annotations are included when available; missing values are NA. The MAVEdb score-set accession defines the retained records; selected effect values, intervals, and FDRs use the full-precision author Dataset EV3 layer and agree with MAVEdb up to API rounding. The other integrated effects are contextual annotations. Raw sequencing reads were not included.