This track is part of the MaveDB track collection. It shows one item per measured variant per MaveDB score set, so a variant measured in several experiments appears once for each of them. A variant that changes an amino acid covers its codon; a variant measured only at the DNA level, for example in an intron, covers the changed bases.
Items are named by gene and amino acid change on the reference protein, for example TP53:R175H, TP53:R175* (stop), TP53:R175= (synonymous) or TP53:R175del, and by their genomic change otherwise. Type a name, a ClinGen allele ID (for example PA106629) or a MaveDB variant ID into the position box to jump to it.
The details page of each item gives its score as submitted to MaveDB, the range of scores in its score set, the change as the experiment reported it (numbered on the sequence that was tested), MaveDB's own mapped terms, the reference protein position used, who placed it, any difference between the tested construct and the reference protein, the ClinGen allele and links to MaveDB.
Items are colored on their own score set's scale, the same scale as the MaveDB Heatmaps: from blue for the lowest score in the score set, through silver for the midpoint between the lowest and the highest, to red for the highest. Scores have no common scale or direction between score sets, so colors can only be compared within one score set.
| Lowest score in the score set | |
| Midpoint between the lowest and highest score | |
| Highest score in the score set |
Well studied genes carry many score sets, so this track can stack hundreds of items on one codon. Use the filters on the track settings page to show one gene, one score set (by its MaveDB ID, for example 00000068-a-1), one assay method or model system, or one way of placement. When too many items are in view, or the view is wider than 200,000 bases, the track shows a density graph instead.
An experiment numbers its variants along the sequence it tested, which is often a fragment, a single domain or a modified copy of the gene, so its position 1 is rarely position 1 of the protein. A variant is shown only if it can be placed on a reference protein position, or on the genome, in one of the ways below. The "Placed by" field of each item says which.
| Placed by | Meaning |
|---|---|
| MaveDB | MaveDB's own mapping, which UCSC checked and agrees with. |
| UCSC: MaveDB offset | The variant has no usable MaveDB mapping (often an amino acid change made by several base changes, which MaveDB does not map), and was placed using the same offset MaveDB used for the rest of the score set. |
| UCSC: assay numbering | MaveDB did not map the score set at protein level. UCSC found where the experiment's amino acids lie in the gene's reference protein. |
| UCSC: corrected MaveDB offset | MaveDB mapped the score set, but its mapped amino acids disagree with the ones the experiment reports, while the experiment's own amino acids fit the reference protein at another position. None of MaveDB's protein-level placements for that score set are used. |
| UCSC: reference term | MaveDB did not map the variant, but the experiment described it on a reference transcript (genome editing score sets often do), and it was placed from that description. |
To find a score set's position on the reference protein, UCSC compares the amino acid the experiment reports at each position (the "Arg" in p.Arg175His) with the reference protein, one fixed shift for the whole score set. MaveDB's own shift is used when it agrees. Otherwise the gene's RefSeq proteins are searched for the one shift at which the experiment's amino acids agree; at least ten positions are needed, and if more than one shift agrees on one protein (as on the repeated ubiquitin sequence), the score set is not placed this way. A construct may differ from the reference at one position, or by a few residues added at one end, such as a tag; variants at those positions are not shown, and the item notes the difference. No alignment is used to place variants.
Every placed amino acid change is then checked twice: the experiment's reference amino acid must equal the reference protein's at that position, and the genome's codon there must encode it. A genomic change must match the genome's reference base. Variants that fail are not shown.
Score sets in which fewer than one in five variants could be placed are not shown, and neither are variants that change several sites at once, frameshifts, insertions and deletions of more than one amino acid, and variants without a score.
MaveDB maps each score set to human reference sequences by aligning the tested sequence to GRCh38 with BLAT, choosing a RefSeq transcript (preferring MANE Select) and computing an offset of the tested sequence on the reference protein (Arbesfeld et al., 2025). Its mapped terms are part of the downloaded data.
The human score sets and their variants were downloaded from the MaveDB API (https://api.mavedb.org/api/v1, documented at api.mavedb.org/docs), with the scores, MaveDB's mapped terms and ClinGen allele IDs. Each variant was placed as described above, using RefSeq proteins and their transcripts (current and historical versions) for codons, and the genome sequence for the checks; variants described on reference transcripts were converted with our hgvsToVcf tool. The steps are in the makeDoc file and the scripts in the MaveDB update directory of our source tree.
The data can be explored interactively in table format with the Table Browser or the Data Integrator and exported from there to spreadsheet or tab-separated tables. From scripts, the data can be accessed through our API, track=mavedb_variants.
For automated download and analysis, the variants are stored in a bigBed file that can be downloaded from our download server. The file for this track is called mavedbVariants.bb. Individual regions or the whole file can be obtained using our tool bigBedToBed, which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain features within a given range, e.g. bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/maveDB/mavedbVariants.bb -chrom=chr17 -start=7675000 -end=7675100 stdout
The original data can be downloaded from MaveDB. Each score set carries its own license, shown on its MaveDB page.
Arbesfeld JA, Da EY, Stevenson JS, Kuzma K, Paul A, Farris T, Capodanno BJ, Grindstaff SB, Riehle K, Saraiva-Agostinho N et al. Mapping MAVE data for use in human genomics applications. Genome Biol. 2025 Jun 25;26(1):179. PMID: 40563119; PMC: PMC12188674
Rubin AF, Stone J, Bianchi AH, Capodanno BJ, Da EY, Dias M, Esposito D, Frazer J, Fu Y, Grindstaff SB et al. MaveDB 2024: a curated community database with over seven million variant effects from multiplexed functional assays. Genome Biol. 2025 Jan 21;26(1):13. PMID: 39838450; PMC: PMC11753097