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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
MTHFR ENST00000376592 38.36 49.65 42.23 0.90 0.66 0.70 1.73 2.02 2.01
SERPINB5 ENST00000382771 38.36 53.70 44.59 0.90 0.63 0.62 1.73 1.70 2.05
COLQ ENST00000383788 38.37 60.32 48.21 0.90 0.53 0.66 1.73 1.39 1.87
ZNF35 ENST00000396056 38.37 30.34 32.54 0.90 1.08 0.89 1.73 1.41 1.61
ABHD14B ENST00000483233 38.38 86.61 63.73 0.90 0.24 0.49 1.73 0.40 1.38
CHRNA3 ENST00000326828 38.38 64.69 50.56 0.90 0.48 0.67 1.73 1.24 1.86
SF3A2 ENST00000221494 38.39 18.01 26.33 0.90 1.52 1.00 1.73 0.74 1.25
CTTNBP2 ENST00000160373 38.39 31.35 33.01 0.90 0.97 0.85 1.73 1.40 1.66
SEZ6L2 ENST00000308713 38.40 20.95 27.83 0.90 1.43 0.87 1.73 0.83 1.28
MOB2 ENST00000329957 38.40 43.92 39.51 0.90 0.61 0.80 1.73 1.97 2.03
NDRG3 ENST00000349004 38.41 21.68 28.23 0.90 1.46 0.81 1.73 0.81 1.29
IL12B ENST00000231228 38.41 49.67 42.30 0.90 0.66 0.70 1.73 2.02 2.01
ZCCHC17 ENST00000373714 38.42 45.25 40.13 0.90 0.70 0.82 1.73 1.98 1.99
APEH ENST00000296456 38.42 45.57 40.27 0.91 0.75 0.80 1.73 1.99 1.99
GSTO1 ENST00000369713 38.43 89.19 65.29 0.91 0.27 0.53 1.73 0.36 1.31
NRBF2 ENST00000277746 38.43 58.16 47.03 0.91 0.54 0.70 1.73 1.45 1.89
PFN4 ENST00000313213 38.44 75.02 56.54 0.92 0.52 0.52 1.72 0.93 1.70
VPS8 ENST00000437079 38.44 22.54 28.66 0.92 1.48 0.80 1.73 0.84 1.34
MYH8 ENST00000403437 38.45 55.47 45.66 0.92 0.57 0.68 1.73 1.60 1.99
PLA2G12B ENST00000373032 38.45 66.38 51.58 0.92 0.54 0.62 1.73 1.20 1.94
CNKSR3 ENST00000607772 38.46 26.62 30.80 0.92 1.20 0.78 1.72 1.12 1.49
ORMDL2 ENST00000243045 38.46 49.41 42.18 0.92 0.65 0.68 1.72 2.01 2.01
LAMB2 ENST00000418109 38.47 34.39 34.66 0.92 0.84 0.90 1.72 1.56 1.76
STOM ENST00000286713 38.47 62.93 49.64 0.92 0.51 0.66 1.72 1.31 1.84
NSG2 ENST00000303177 38.48 20.00 27.37 0.92 1.44 0.96 1.72 0.73 1.27

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