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Genes Fold Enrichment Color Codes
  • Gene Name, Canonical Transcript - gene identifiers from gnomAD database (Build 37)
  • GeVIR % - gene rank measured in percentiles based on Gene Variation Intolerance Ranking (GeVIR) (low values indicate more variation intolerant genes, which is also true for "LOEUF %" and "VIRLoF %"). GeVIR is a method which we developed and applied on a list of 19,361 genes to sort them based on number, length and evolutionary conservation of regions without functional variants (i.e. between two missense, loss-of-function, insertion or delition variants) in gnomAD database (version 2.0.1). Only canonical transcripts were analysed.
  • LOEUF % - gene rank measured in percentiles based gnomAD loss-of-function observed/expected upper bound fraction (LOEUF) (see Figure 1). For more information about this metric, please read "Constraint" section of MacArthur Lab blog post. If you use this metric please cite gnomAD flagship paper and use most up-to-date values from gnomAD website.

    LoF observed/expected (o/e) upper Confidence Interval (CI)

    Figure 1. Screenshot of ELN gene constraint metrics from gnomAD browser

  • VIRLoF % - gene rank measured in percentiles based on both GeVIR and gnomAD LOEUF (shows the best overall performance, see Figure 2). If you use this metric please cite both GeVIR and gnomAD flagship paper.
  • GeVIR AD, LOEUF AD, VIRLoF AD, GeVIR AR, LOEUF AR, VIRLoF AR - to help users interpret gene ranks, we calculated fold enrichment of Autosomal Dominant (AD) and Autosomal Recessive (AR) genes with known molecular basis of disorder in OMIM in a range of +-5% of gene X (see Figure 2). Statistical significant fold enrichements (Fisher Exact Test p-value < 1e-5) are shown in bold in the table. For example CDK19 gene's GeVIR % is 2.37, so examined range is from 0 (2.37-5, rounded to minimal percentile) to 7.37% (2.37+5). Genes in this range are ~4 times more often (4.05 fold enrichement) associated with AD diseases and ~4 times less often (0.25 fold enrichement) associated with AR diseases. Both enrichment of AD genes and deficiency of AR genes is statistical significant. Thus GeVIR metric adds supportive evidence that CDK19 is more likely to be associated with AD than AR disease.

    Gene Percentiles AD AR Fold Enrichment

    Figure 2. Fold Enrichment of known Autosomal Dominant (AD) and Autosomal Recessive (AR) genes of each gene in the ranked lists (GeVIR, LOEUF, VIRLoF. AD genes are enriched among top ranked genes (lowest percentiles), whereas AR genes are enriched among middle ranked genes (approximetly 35-65 percentiles). Combined metric (VIRLoF, purple) shows the best perfornance, i.e. high ranked genes are more often associated with AD than AR diseases, low ranked genes are less often associated with both AD and AR diseases.
Gene Name Canonical Transcript GeVIR % LOEUF % VIRLoF % GeVIR AD LOEUF AD VIRLoF AD GeVIR AR LOEUF AR VIRLoF AR
TMEM167A ENST00000502346 41.71 88.88 67.04 0.81 0.25 0.52 1.73 0.35 1.17
SLC35A5 ENST00000492406 41.72 63.97 52.09 0.81 0.48 0.61 1.73 1.20 1.93
MT3 ENST00000200691 41.72 79.37 61.17 0.80 0.38 0.43 1.73 0.67 1.50
MYF6 ENST00000228641 41.73 61.79 50.82 0.80 0.57 0.67 1.73 1.37 1.84
MRC2 ENST00000303375 41.73 12.93 25.41 0.80 2.07 1.04 1.73 0.59 1.17
GUCY1A3 ENST00000296518 41.74 44.79 41.50 0.80 0.68 0.73 1.73 1.97 2.02
EVL ENST00000392920 41.74 7.93 22.99 0.80 2.53 1.20 1.73 0.44 0.98
MCCC1 ENST00000265594 41.75 48.33 43.40 0.80 0.63 0.63 1.73 2.01 2.00
UBA7 ENST00000333486 41.75 50.62 44.81 0.80 0.63 0.66 1.73 1.95 2.04
FAM189A2 ENST00000257515 41.76 60.44 50.12 0.80 0.53 0.63 1.73 1.41 1.90
DRAM2 ENST00000286692 41.76 62.05 50.96 0.80 0.56 0.66 1.73 1.37 1.85
COL8A1 ENST00000261037 41.77 26.40 32.29 0.80 1.16 0.90 1.73 1.09 1.61
USP44 ENST00000258499 41.77 58.35 48.94 0.80 0.54 0.71 1.73 1.41 1.84
ORC4 ENST00000392857 41.78 58.83 49.22 0.80 0.54 0.72 1.73 1.41 1.84
PYCR1 ENST00000329875 41.79 68.19 54.56 0.80 0.52 0.56 1.73 1.21 1.73
ANGPT2 ENST00000325203 41.79 16.95 27.47 0.80 1.66 0.97 1.73 0.72 1.27
VAT1 ENST00000355653 41.80 43.41 40.77 0.80 0.61 0.81 1.73 1.95 2.04
MRPL47 ENST00000476781 41.80 46.73 42.52 0.80 0.73 0.68 1.73 1.97 2.01
STUB1 ENST00000219548 41.81 34.95 36.48 0.80 0.76 0.84 1.74 1.55 1.90
NIPAL1 ENST00000295461 41.81 79.08 61.07 0.80 0.39 0.43 1.74 0.69 1.53
SLC43A3 ENST00000395123 41.82 46.68 42.50 0.80 0.73 0.68 1.74 1.97 2.00
TMEM145 ENST00000301204 41.82 45.25 41.75 0.80 0.70 0.72 1.73 1.98 2.00
ARHGAP36 ENST00000276211 41.83 18.62 28.42 0.80 1.48 0.78 1.74 0.75 1.29
PDXDC1 ENST00000396410 41.83 40.80 39.69 0.80 0.62 0.80 1.74 1.78 2.04
TMEM38A ENST00000187762 41.84 66.06 53.34 0.80 0.56 0.62 1.74 1.21 1.86

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