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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
PKD2L1 ENST00000318222 49.72 68.58 59.40 0.54 0.53 0.49 1.84 1.19 1.71
SNTG1 ENST00000522124 49.72 19.82 32.94 0.54 1.42 0.86 1.84 0.74 1.67
EBAG9 ENST00000337573 49.73 37.98 42.08 0.54 0.77 0.71 1.84 1.71 1.99
RPL13A ENST00000391857 49.73 21.92 34.01 0.54 1.46 0.89 1.84 0.81 1.72
SLC24A5 ENST00000341459 49.74 61.32 55.15 0.54 0.54 0.51 1.84 1.39 1.74
MIF4GD ENST00000577542 49.74 78.35 65.63 0.54 0.43 0.51 1.84 0.73 1.29
INO80C ENST00000441607 49.75 72.45 61.85 0.54 0.48 0.47 1.84 1.03 1.46
TECPR1 ENST00000447648 49.75 23.91 35.01 0.54 1.39 0.87 1.84 0.95 1.73
NT5C1B ENST00000359846 49.76 51.18 49.33 0.54 0.66 0.70 1.84 1.91 1.84
ZPLD1 ENST00000306176 49.76 55.28 51.67 0.54 0.57 0.62 1.84 1.62 1.94
FGFR4 ENST00000292408 49.77 47.48 47.39 0.54 0.63 0.65 1.83 2.01 1.85
ADC ENST00000294517 49.78 48.54 48.01 0.54 0.65 0.67 1.84 2.01 1.88
PTPN21 ENST00000556564 49.78 32.63 39.54 0.54 0.85 0.80 1.83 1.47 2.03
SELT ENST00000471696 49.79 46.28 46.75 0.54 0.73 0.67 1.83 2.04 1.87
BCDIN3D ENST00000333924 49.79 72.64 61.94 0.54 0.47 0.48 1.83 1.03 1.45
MCM4 ENST00000262105 49.80 25.34 35.69 0.54 1.28 0.85 1.83 1.03 1.76
CNKSR1 ENST00000361530 49.80 69.09 59.81 0.54 0.56 0.49 1.83 1.14 1.63
DMRTC2 ENST00000269945 49.81 21.19 33.67 0.54 1.46 0.90 1.82 0.81 1.72
TRIM59 ENST00000309784 49.81 46.59 46.93 0.54 0.75 0.70 1.82 2.01 1.87
ASNSD1 ENST00000260952 49.82 78.13 65.50 0.54 0.43 0.52 1.82 0.73 1.28
MST1R ENST00000296474 49.82 69.82 60.28 0.54 0.54 0.47 1.82 1.14 1.60
GPRC6A ENST00000310357 49.83 71.66 61.42 0.54 0.52 0.44 1.82 1.07 1.47
HEPHL1 ENST00000315765 49.83 65.32 57.53 0.54 0.51 0.52 1.82 1.25 1.66
HTR6 ENST00000289753 49.84 70.02 60.39 0.54 0.53 0.44 1.82 1.14 1.58
TMEM8C ENST00000339996 49.84 70.21 60.58 0.54 0.53 0.44 1.82 1.12 1.58

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