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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
CLVS1 ENST00000519846 19.76 19.67 17.63 1.56 1.42 1.64 1.00 0.74 0.77
GTF3C1 ENST00000356183 19.77 4.51 9.59 1.56 3.26 2.28 0.99 0.32 0.40
MID2 ENST00000262843 19.77 22.70 19.20 1.56 1.47 1.54 0.99 0.88 0.85
TGFB1I1 ENST00000394863 19.78 29.24 22.68 1.56 1.14 1.18 0.99 1.36 0.97
DSCAM ENST00000400454 19.78 4.50 9.57 1.54 3.27 2.28 0.99 0.32 0.40
HSPA4 ENST00000304858 19.79 6.88 10.98 1.54 2.62 2.21 0.99 0.37 0.44
ZSWIM5 ENST00000359600 19.79 18.25 16.86 1.54 1.49 1.70 0.99 0.74 0.70
CNTN1 ENST00000551295 19.80 15.39 15.38 1.54 1.90 1.81 1.00 0.67 0.66
NKX6-1 ENST00000295886 19.80 58.74 37.53 1.54 0.54 0.84 1.00 1.44 2.01
WDR11 ENST00000263461 19.81 27.05 21.57 1.54 1.23 1.28 0.99 1.12 0.93
EIF3H ENST00000521861 19.81 30.33 23.18 1.54 1.08 1.19 0.99 1.41 1.02
STRIP1 ENST00000369795 19.82 28.61 22.39 1.54 1.18 1.16 0.99 1.29 0.96
HMG20B ENST00000333651 19.82 22.95 19.42 1.54 1.47 1.54 0.99 0.90 0.84
ACAP1 ENST00000158762 19.83 21.48 18.65 1.54 1.42 1.58 0.99 0.79 0.81
RBM15 ENST00000369784 19.83 10.36 12.66 1.54 2.24 2.19 0.99 0.50 0.52
RLIM ENST00000332687 19.84 8.38 11.74 1.54 2.52 2.21 0.99 0.46 0.46
DTNA ENST00000598334 19.84 16.23 15.87 1.54 1.80 1.77 0.99 0.69 0.66
ULK2 ENST00000395544 19.85 27.28 21.71 1.54 1.25 1.25 0.99 1.15 0.92
B3GAT1 ENST00000524765 19.85 32.91 24.42 1.54 0.82 1.08 0.99 1.44 1.08
RASGRP4 ENST00000587738 19.86 23.71 19.82 1.54 1.39 1.49 0.99 0.93 0.85
NR1D2 ENST00000312521 19.86 32.84 24.40 1.53 0.84 1.08 0.99 1.44 1.08
DMC1 ENST00000216024 19.87 40.41 28.31 1.53 0.61 0.78 0.99 1.76 1.28
PHF20L1 ENST00000395386 19.88 5.61 10.34 1.53 2.99 2.19 0.99 0.33 0.43
PEX16 ENST00000241041 19.88 43.60 29.93 1.53 0.62 0.86 0.99 1.95 1.44
PVRL4 ENST00000368012 19.89 19.91 17.80 1.53 1.44 1.66 0.99 0.73 0.78

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