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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
KIAA0895L ENST00000290881 49.33 38.61 42.20 0.57 0.73 0.68 1.81 1.66 2.02
TRIM69 ENST00000559390 49.34 62.38 55.52 0.57 0.53 0.51 1.80 1.33 1.74
CPA5 ENST00000485477 49.34 37.58 41.69 0.57 0.80 0.72 1.81 1.68 2.01
MOSPD3 ENST00000393950 49.35 68.01 58.79 0.57 0.52 0.51 1.81 1.19 1.65
KIF6 ENST00000287152 49.35 62.19 55.42 0.57 0.52 0.49 1.81 1.35 1.71
TGFBI ENST00000442011 49.36 40.61 43.33 0.57 0.63 0.63 1.81 1.77 2.00
PDE9A ENST00000291539 49.36 25.34 35.50 0.57 1.28 0.85 1.81 1.03 1.77
GTPBP4 ENST00000360803 49.37 0.71 23.12 0.57 4.08 1.20 1.81 0.28 1.00
ADA ENST00000372874 49.37 69.41 59.74 0.57 0.56 0.49 1.81 1.13 1.66
FMN2 ENST00000319653 49.38 10.38 28.07 0.57 2.25 0.81 1.80 0.50 1.29
CCHCR1 ENST00000396268 49.38 46.15 46.41 0.57 0.73 0.67 1.80 2.04 1.91
SLC44A4 ENST00000229729 49.39 48.91 47.97 0.57 0.63 0.67 1.80 2.04 1.87
SASH1 ENST00000367467 49.39 21.28 33.48 0.57 1.42 0.89 1.80 0.81 1.72
FAM212A ENST00000333323 49.40 72.70 61.78 0.57 0.47 0.46 1.80 1.03 1.46
HYLS1 ENST00000425380 49.40 75.99 63.97 0.57 0.43 0.52 1.79 0.86 1.39
ADCK4 ENST00000324464 49.41 61.41 55.01 0.57 0.54 0.51 1.80 1.40 1.73
LRMP ENST00000354454 49.41 48.65 47.87 0.57 0.63 0.66 1.80 2.00 1.90
GPR45 ENST00000258456 49.42 45.54 46.20 0.56 0.72 0.67 1.80 1.99 1.94
HIST1H2BD ENST00000289316 49.42 97.31 76.47 0.56 0.23 0.38 1.80 0.19 0.61
ATG4C ENST00000317868 49.43 77.99 65.16 0.56 0.42 0.52 1.80 0.77 1.31
TMEM41A ENST00000421852 49.43 65.08 57.16 0.56 0.51 0.52 1.80 1.24 1.69
SLC9C2 ENST00000367714 49.44 21.62 33.69 0.56 1.44 0.90 1.80 0.81 1.73
GMPPB ENST00000308375 49.44 63.95 56.52 0.56 0.48 0.52 1.81 1.21 1.70
FITM1 ENST00000267426 49.45 73.93 62.60 0.56 0.53 0.48 1.80 1.02 1.40
RHBDD2 ENST00000006777 49.46 27.61 36.69 0.56 1.27 0.82 1.80 1.17 1.93

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