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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
CCDC25 ENST00000356537 18.99 40.39 27.84 1.58 0.61 0.87 0.95 1.76 1.28
TPT1 ENST00000530705 18.99 23.64 19.30 1.58 1.39 1.53 0.95 0.93 0.85
WAC ENST00000354911 19.00 0.76 7.24 1.58 4.11 2.81 0.95 0.27 0.33
FMNL3 ENST00000335154 19.00 16.69 15.68 1.58 1.71 1.77 0.95 0.71 0.67
NKAIN1 ENST00000373736 19.01 33.42 24.23 1.58 0.84 1.13 0.95 1.52 1.05
PEX3 ENST00000367591 19.01 27.63 21.46 1.58 1.28 1.30 0.95 1.17 0.91
VAMP1 ENST00000396308 19.02 62.70 39.24 1.58 0.51 0.78 0.95 1.31 2.04
SLC16A1 ENST00000538576 19.02 45.90 30.72 1.58 0.75 0.78 0.95 2.02 1.48
FAM155A ENST00000375915 19.03 12.63 13.43 1.58 2.09 2.05 0.95 0.58 0.55
GCH1 ENST00000491895 19.03 18.12 16.38 1.58 1.52 1.71 0.95 0.74 0.68
DNAJC13 ENST00000260818 19.04 4.95 9.41 1.58 3.26 2.29 0.95 0.32 0.40
LMOD1 ENST00000367288 19.04 19.18 16.96 1.58 1.49 1.67 0.95 0.76 0.71
UGT8 ENST00000310836 19.05 32.73 23.92 1.58 0.84 1.09 0.95 1.44 1.04
STK40 ENST00000373129 19.05 8.27 11.34 1.58 2.54 2.20 0.95 0.45 0.45
ETNPPL ENST00000296486 19.06 40.79 28.12 1.58 0.62 0.81 0.95 1.78 1.28
CMAS ENST00000229329 19.06 17.24 15.98 1.58 1.61 1.76 0.95 0.75 0.66
FAM76A ENST00000010299 19.07 40.57 28.02 1.58 0.63 0.82 0.95 1.76 1.27
PANX2 ENST00000395842 19.07 69.34 42.47 1.58 0.56 0.68 0.95 1.14 1.99
RAB11FIP2 ENST00000355624 19.08 15.86 15.23 1.58 1.89 1.83 0.95 0.68 0.65
CPNE5 ENST00000244751 19.08 28.98 22.17 1.58 1.15 1.15 0.95 1.31 0.96
C7orf25 ENST00000431882 19.09 29.54 22.49 1.58 1.10 1.16 0.95 1.39 0.98
NUP98 ENST00000324932 19.10 1.81 7.83 1.58 3.79 2.61 0.95 0.26 0.35
SPCS1 ENST00000233025 19.10 60.31 37.98 1.58 0.53 0.85 0.95 1.39 2.02
WNK3 ENST00000354646 19.11 5.46 9.79 1.58 3.04 2.29 0.95 0.33 0.40
NCKAP1L ENST00000293373 19.11 13.44 13.96 1.58 2.05 2.06 0.95 0.60 0.59

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