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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
TF ENST00000402696 52.17 39.90 44.57 0.59 0.63 0.62 1.83 1.69 2.04
SLC25A32 ENST00000297578 52.18 72.98 63.86 0.59 0.51 0.49 1.83 1.03 1.39
ZMAT1 ENST00000372782 52.18 43.10 46.30 0.59 0.61 0.67 1.83 1.91 1.91
PLEKHH2 ENST00000282406 52.19 49.90 50.03 0.59 0.66 0.61 1.83 2.02 1.92
APMAP ENST00000217456 52.19 71.88 63.11 0.59 0.51 0.49 1.82 1.07 1.39
WFDC5 ENST00000372789 52.20 72.36 63.45 0.59 0.51 0.51 1.82 1.03 1.38
LGSN ENST00000370657 52.20 81.05 68.63 0.59 0.35 0.46 1.82 0.55 1.05
SLC23A3 ENST00000455516 52.21 39.60 44.39 0.59 0.68 0.59 1.82 1.65 2.03
PRKAG3 ENST00000529249 52.21 64.68 58.50 0.59 0.48 0.51 1.82 1.24 1.64
VWA8 ENST00000379310 52.22 62.95 57.56 0.59 0.51 0.51 1.82 1.31 1.66
NICN1 ENST00000273598 52.22 48.70 49.33 0.59 0.63 0.70 1.82 1.99 1.84
SCLT1 ENST00000281142 52.23 48.36 49.24 0.59 0.63 0.72 1.82 2.00 1.85
TMEM209 ENST00000397622 52.23 54.92 52.99 0.59 0.57 0.61 1.82 1.63 1.88
AK9 ENST00000424296 52.24 38.79 43.92 0.59 0.70 0.61 1.82 1.66 2.02
DNALI1 ENST00000296218 52.24 79.53 67.75 0.59 0.38 0.52 1.82 0.66 1.12
FANCI ENST00000310775 52.25 54.73 52.80 0.59 0.58 0.61 1.82 1.64 1.88
MPI ENST00000352410 52.25 67.35 60.27 0.59 0.56 0.47 1.82 1.21 1.60
TMLHE ENST00000334398 52.26 64.58 58.48 0.59 0.48 0.51 1.83 1.22 1.64
CHM ENST00000357749 52.26 5.40 26.99 0.59 3.05 1.00 1.83 0.33 1.28
GPR17 ENST00000544369 52.27 72.21 63.39 0.59 0.52 0.49 1.83 1.04 1.37
FAM26E ENST00000368599 52.28 66.42 59.67 0.59 0.56 0.49 1.83 1.20 1.67
CARD10 ENST00000403299 52.28 21.93 35.32 0.61 1.46 0.87 1.83 0.81 1.75
RAB38 ENST00000243662 52.29 75.40 65.38 0.61 0.46 0.53 1.82 0.90 1.32
PON1 ENST00000222381 52.29 71.24 62.68 0.61 0.53 0.51 1.82 1.07 1.39
TMEM95 ENST00000330767 52.30 80.71 68.49 0.61 0.37 0.47 1.82 0.57 1.06

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