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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
PLAC8L1 ENST00000311450 28.15 71.35 48.64 1.16 0.53 0.67 1.47 1.05 1.85
PHOSPHO2 ENST00000359744 28.16 83.40 55.44 1.16 0.27 0.51 1.47 0.47 1.72
SEMA3D ENST00000284136 28.16 34.82 29.65 1.16 0.76 0.85 1.47 1.55 1.40
ADSL ENST00000216194 28.17 55.15 40.01 1.16 0.57 0.82 1.47 1.62 1.99
FECH ENST00000382873 28.18 31.45 28.00 1.16 0.96 0.82 1.47 1.42 1.27
GBAS ENST00000322090 28.18 61.02 42.92 1.16 0.54 0.67 1.47 1.40 1.99
MBD3 ENST00000156825 28.19 9.57 16.72 1.16 2.49 1.68 1.47 0.50 0.70
APAF1 ENST00000551964 28.19 23.19 23.76 1.16 1.46 1.13 1.47 0.91 1.02
ERC1 ENST00000397203 28.20 27.52 26.03 1.16 1.25 0.99 1.47 1.17 1.25
HIST1H3H ENST00000369163 28.20 93.61 61.64 1.16 0.28 0.46 1.47 0.28 1.47
ESD ENST00000378720 28.21 66.24 45.92 1.16 0.53 0.70 1.47 1.20 1.97
CD163 ENST00000359156 28.21 21.11 22.80 1.16 1.47 1.19 1.47 0.82 0.98
MYRIP ENST00000302541 28.22 29.04 26.79 1.16 1.14 0.96 1.47 1.31 1.28
TYRO3 ENST00000263798 28.22 32.64 28.57 1.16 0.85 0.80 1.47 1.46 1.35
ATP7A ENST00000341514 28.23 6.59 15.17 1.16 2.63 1.83 1.47 0.37 0.64
TCEAL8 ENST00000372685 28.23 70.06 48.02 1.16 0.53 0.67 1.47 1.14 1.89
HGS ENST00000329138 28.24 22.36 23.40 1.16 1.51 1.19 1.47 0.82 1.00
PCDHGC5 ENST00000252087 28.24 40.07 32.35 1.16 0.63 0.91 1.47 1.70 1.61
EIF2B5 ENST00000273783 28.25 20.04 22.30 1.16 1.43 1.16 1.47 0.73 0.96
L1CAM ENST00000370060 28.25 2.37 12.84 1.16 3.62 2.11 1.48 0.29 0.53
HIST1H2AC ENST00000602637 28.26 55.24 40.06 1.16 0.57 0.82 1.48 1.62 1.99
CTNND1 ENST00000399050 28.26 4.86 14.27 1.16 3.28 2.01 1.48 0.31 0.60
GLCCI1 ENST00000223145 28.27 28.89 26.75 1.16 1.15 0.97 1.48 1.31 1.27
VHL ENST00000256474 28.27 58.13 41.42 1.16 0.53 0.73 1.48 1.46 2.02
KIF1C ENST00000320785 28.28 14.94 19.62 1.18 1.92 1.53 1.48 0.62 0.85

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