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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
OR2Y1 ENST00000307832 81.87 99.04 93.24 0.32 0.15 0.14 0.57 0.14 0.15
MLYCD ENST00000262430 81.88 45.58 65.17 0.32 0.75 0.52 0.57 1.98 1.31
SFTPA1 ENST00000419470 81.88 69.92 79.23 0.32 0.53 0.38 0.57 1.14 0.54
OR3A2 ENST00000408891 81.89 81.89 85.24 0.32 0.35 0.34 0.57 0.51 0.36
MUC15 ENST00000436318 81.89 70.53 79.48 0.32 0.52 0.38 0.57 1.08 0.52
SH2D3A ENST00000245908 81.90 57.35 72.32 0.32 0.54 0.44 0.57 1.49 0.82
ATP5SL ENST00000417807 81.90 76.63 82.67 0.32 0.42 0.32 0.57 0.83 0.43
OR4S1 ENST00000319988 81.91 91.03 89.61 0.32 0.25 0.18 0.57 0.36 0.23
ACSM2A ENST00000573854 81.91 75.72 82.19 0.32 0.44 0.35 0.57 0.88 0.45
NES ENST00000368223 81.92 24.22 52.32 0.32 1.32 0.61 0.57 0.98 1.91
GLI4 ENST00000340042 81.92 48.12 66.75 0.32 0.63 0.53 0.57 1.98 1.20
C19orf54 ENST00000378313 81.93 67.37 77.85 0.32 0.56 0.38 0.57 1.20 0.54
ITFG3 ENST00000600536 81.93 65.59 76.90 0.32 0.53 0.35 0.57 1.22 0.60
MTL5 ENST00000255087 81.94 45.75 65.38 0.32 0.75 0.53 0.57 2.02 1.32
ADAD2 ENST00000268624 81.94 63.83 75.90 0.32 0.49 0.38 0.57 1.21 0.62
LCA5L ENST00000358268 81.95 59.04 73.27 0.32 0.51 0.43 0.57 1.43 0.79
DHDH ENST00000221403 81.95 79.39 83.96 0.32 0.38 0.35 0.57 0.67 0.43
SRMS ENST00000217188 81.96 80.07 84.34 0.32 0.37 0.33 0.57 0.60 0.40
GBP4 ENST00000355754 81.96 68.11 78.29 0.32 0.52 0.38 0.57 1.20 0.55
EMR2 ENST00000315576 81.97 71.26 79.94 0.32 0.53 0.35 0.57 1.07 0.52
PCP2 ENST00000311069 81.97 86.55 87.40 0.32 0.24 0.28 0.57 0.42 0.31
ZNF177 ENST00000541595 81.98 61.36 74.59 0.32 0.54 0.40 0.57 1.40 0.68
PZP ENST00000261336 81.98 51.69 68.87 0.30 0.61 0.46 0.57 1.87 1.04
ACTL8 ENST00000375406 81.99 65.96 77.14 0.30 0.56 0.35 0.57 1.23 0.59
LYRM5 ENST00000381356 81.99 97.15 92.26 0.30 0.24 0.14 0.57 0.18 0.15

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