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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
CNTN4 ENST00000397461 32.29 26.84 27.72 0.99 1.23 0.92 1.70 1.12 1.27
KLF13 ENST00000307145 32.29 51.48 40.17 0.99 0.63 0.82 1.70 1.87 1.99
BLM ENST00000355112 32.30 38.40 33.51 0.99 0.75 0.89 1.70 1.71 1.72
LRSAM1 ENST00000323301 32.30 39.61 34.15 0.99 0.68 0.89 1.70 1.65 1.75
NUDT22 ENST00000279206 32.31 73.48 52.14 0.99 0.53 0.61 1.70 1.03 1.91
CD79B ENST00000392795 32.31 18.94 23.73 0.99 1.52 1.15 1.70 0.76 1.02
SNRPA ENST00000243563 32.32 74.82 52.97 0.99 0.53 0.61 1.70 0.95 1.87
TENM4 ENST00000278550 32.32 4.35 16.14 0.99 3.26 1.71 1.70 0.32 0.66
CLSPN ENST00000318121 32.33 19.43 23.90 0.99 1.46 1.09 1.70 0.74 1.04
UROD ENST00000246337 32.33 62.22 45.98 0.99 0.53 0.70 1.71 1.34 1.97
ZNF638 ENST00000409544 32.34 3.88 15.95 0.99 3.29 1.77 1.71 0.31 0.66
ASCC2 ENST00000397771 32.34 20.12 24.24 0.99 1.43 1.13 1.71 0.75 1.05
SENP6 ENST00000447266 32.35 7.14 17.63 0.99 2.58 1.64 1.71 0.37 0.77
ZW10 ENST00000200135 32.35 26.82 27.75 0.99 1.23 0.90 1.71 1.12 1.27
ZNF583 ENST00000333201 32.36 31.07 29.90 0.99 1.04 0.86 1.71 1.36 1.44
CPT1B ENST00000360719 32.36 46.19 37.53 0.99 0.73 0.84 1.70 2.03 2.01
NTN1 ENST00000173229 32.37 2.58 15.24 0.99 3.54 1.83 1.70 0.29 0.65
PDXK ENST00000291565 32.37 20.58 24.54 0.99 1.44 1.06 1.70 0.76 1.09
COG7 ENST00000307149 32.38 35.50 32.13 0.99 0.77 0.89 1.70 1.57 1.60
STRN4 ENST00000391910 32.38 10.97 19.75 0.99 2.10 1.52 1.70 0.52 0.85
NRROS ENST00000328557 32.39 26.28 27.44 0.99 1.19 0.96 1.70 1.08 1.27
COX11 ENST00000299335 32.40 45.41 37.15 0.99 0.68 0.81 1.70 2.01 1.97
MPZL3 ENST00000278949 32.40 96.67 66.19 0.97 0.23 0.52 1.70 0.20 1.20
PSMD13 ENST00000431206 32.41 5.68 16.93 0.97 2.96 1.67 1.70 0.34 0.71
SIK1 ENST00000270162 32.41 12.70 20.68 0.97 2.10 1.47 1.70 0.58 0.88

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