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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
TDRD1 ENST00000251864 25.83 4.12 12.52 1.34 3.26 2.21 1.21 0.32 0.51
LDHB ENST00000396076 25.84 64.64 43.59 1.34 0.48 0.62 1.20 1.23 2.01
USP25 ENST00000285679 25.84 14.58 18.17 1.35 2.04 1.64 1.20 0.61 0.79
COL4A5 ENST00000328300 25.85 5.04 13.03 1.35 3.23 2.09 1.20 0.32 0.52
PIAS4 ENST00000262971 25.85 1.60 11.42 1.35 3.85 2.19 1.20 0.26 0.45
SERPINC1 ENST00000367698 25.86 3.27 12.13 1.35 3.44 2.28 1.20 0.27 0.48
LHX4 ENST00000263726 25.86 36.01 29.10 1.35 0.80 0.84 1.20 1.59 1.32
ELFN2 ENST00000402918 25.87 13.75 17.71 1.35 2.06 1.66 1.20 0.59 0.78
ATP8A2 ENST00000381655 25.87 29.60 25.90 1.35 1.10 1.01 1.20 1.39 1.23
SGPL1 ENST00000373202 25.88 29.88 26.04 1.37 1.14 0.99 1.20 1.40 1.25
SLC2A13 ENST00000280871 25.88 14.02 17.87 1.37 2.06 1.68 1.20 0.59 0.77
KIAA0319L ENST00000325722 25.89 21.83 21.98 1.37 1.47 1.19 1.20 0.81 0.96
ADCYAP1R1 ENST00000396211 25.89 41.68 31.98 1.37 0.61 0.90 1.20 1.80 1.59
NETO2 ENST00000562435 25.90 24.31 23.19 1.37 1.32 1.19 1.20 0.99 1.02
SNX9 ENST00000392185 25.90 16.59 19.21 1.37 1.76 1.54 1.21 0.71 0.86
SPTY2D1 ENST00000336349 25.91 15.65 18.80 1.37 1.87 1.57 1.21 0.69 0.82
ZCCHC24 ENST00000372336 25.91 14.91 18.34 1.37 1.94 1.66 1.21 0.62 0.80
ASB8 ENST00000317697 25.92 70.98 47.20 1.37 0.49 0.67 1.21 1.06 1.89
LARS ENST00000394434 25.92 26.66 24.35 1.37 1.18 1.09 1.21 1.12 1.07
GLS2 ENST00000311966 25.93 44.90 33.57 1.37 0.68 0.87 1.22 1.99 1.72
TMBIM6 ENST00000423828 25.93 37.55 29.92 1.37 0.80 0.86 1.22 1.67 1.44
TNFAIP6 ENST00000243347 25.94 68.21 45.78 1.37 0.52 0.68 1.22 1.21 1.98
ATP6AP2 ENST00000378438 25.94 19.52 20.89 1.37 1.43 1.44 1.22 0.74 0.87
HEPACAM ENST00000298251 25.95 21.21 21.71 1.37 1.44 1.25 1.22 0.81 0.93
KCNJ5 ENST00000529694 25.95 59.79 41.08 1.37 0.52 0.76 1.22 1.37 2.05

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