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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
RPL17-C18orf32 ENST00000584895 24.93 23.87 22.59 1.38 1.39 1.18 1.12 0.95 0.96
FERMT3 ENST00000279227 24.93 26.91 23.96 1.38 1.23 1.09 1.12 1.12 1.05
TBC1D20 ENST00000354200 24.94 16.30 18.60 1.38 1.78 1.58 1.12 0.70 0.81
FGD6 ENST00000343958 24.94 27.27 24.13 1.38 1.25 1.11 1.12 1.15 1.06
GRID1 ENST00000327946 24.95 6.81 13.50 1.39 2.62 2.05 1.12 0.37 0.57
NCOA6 ENST00000374796 24.95 7.76 14.03 1.39 2.53 2.04 1.12 0.43 0.60
PKIG ENST00000372889 24.96 71.01 46.67 1.39 0.49 0.66 1.12 1.07 1.87
USP51 ENST00000500968 24.96 35.24 28.27 1.39 0.76 0.80 1.12 1.58 1.29
IFRD1 ENST00000403825 24.97 31.80 26.48 1.39 0.94 0.99 1.12 1.48 1.25
TRIM32 ENST00000450136 24.97 44.81 33.03 1.39 0.68 0.85 1.12 1.97 1.66
KCNJ15 ENST00000328656 24.98 44.95 33.11 1.39 0.68 0.87 1.12 1.97 1.68
HEY2 ENST00000368364 24.98 18.59 19.88 1.39 1.48 1.47 1.12 0.76 0.84
ANAPC16 ENST00000299381 24.99 75.62 49.21 1.39 0.44 0.72 1.12 0.91 1.84
DRG2 ENST00000225729 24.99 43.41 32.41 1.39 0.61 0.91 1.12 1.95 1.61
TUFM ENST00000313511 25.00 39.22 30.30 1.39 0.70 0.84 1.12 1.63 1.44
TSPAN12 ENST00000222747 25.00 21.65 21.47 1.39 1.46 1.32 1.12 0.81 0.91
ID2 ENST00000234091 25.01 42.59 31.99 1.39 0.59 0.90 1.12 1.89 1.59
MAEL ENST00000367872 25.01 31.61 26.44 1.39 0.95 1.01 1.12 1.44 1.25
CDADC1 ENST00000251108 25.02 64.15 42.90 1.39 0.49 0.67 1.13 1.21 1.99
COX7C ENST00000509578 25.02 61.38 41.37 1.39 0.54 0.73 1.13 1.40 2.03
UXS1 ENST00000283148 25.03 31.63 26.42 1.39 0.95 1.01 1.13 1.44 1.26
PTGFRN ENST00000393203 25.03 26.93 24.03 1.38 1.23 1.10 1.13 1.12 1.06
SPTLC1 ENST00000262554 25.04 54.52 38.06 1.38 0.61 0.85 1.13 1.65 2.02
ADAMTS2 ENST00000251582 25.05 12.48 16.62 1.38 2.07 1.72 1.13 0.59 0.70
EHMT1 ENST00000460843 25.05 0.42 10.30 1.38 4.14 2.19 1.13 0.28 0.42

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