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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
GNMT ENST00000372808 51.66 46.23 47.77 0.58 0.73 0.65 1.85 2.03 1.88
CH25H ENST00000371852 51.66 44.94 47.02 0.58 0.68 0.70 1.85 1.98 1.88
OXGR1 ENST00000298440 51.67 81.54 68.59 0.58 0.33 0.47 1.85 0.52 1.05
HIST1H2AG ENST00000359193 51.67 96.76 77.42 0.58 0.23 0.35 1.85 0.19 0.58
UBE2T ENST00000367274 51.68 70.72 61.94 0.58 0.48 0.48 1.84 1.09 1.45
CEP112 ENST00000392769 51.68 60.13 55.59 0.58 0.52 0.53 1.84 1.39 1.75
ALDH2 ENST00000261733 51.69 57.60 54.14 0.58 0.57 0.59 1.84 1.48 1.75
IGF2R ENST00000356956 51.69 6.92 27.43 0.58 2.61 0.96 1.83 0.37 1.27
NMNAT1 ENST00000377205 51.70 49.47 49.49 0.58 0.66 0.67 1.83 2.03 1.83
AQP1 ENST00000311813 51.70 49.15 49.32 0.58 0.66 0.70 1.82 2.04 1.85
TPMT ENST00000309983 51.71 61.21 56.19 0.58 0.53 0.49 1.82 1.40 1.77
TBRG4 ENST00000258770 51.71 36.38 42.32 0.58 0.82 0.70 1.82 1.63 2.01
PNOC ENST00000301908 51.72 68.49 60.65 0.58 0.52 0.44 1.82 1.20 1.60
NCOR2 ENST00000405201 51.72 3.94 25.98 0.58 3.28 0.99 1.82 0.32 1.25
CRTAP ENST00000320954 51.73 42.56 45.84 0.58 0.59 0.68 1.82 1.88 1.97
DCAF13 ENST00000297579 51.73 48.84 49.20 0.58 0.63 0.72 1.82 2.03 1.84
DSG3 ENST00000257189 51.74 61.15 56.20 0.58 0.53 0.49 1.82 1.40 1.77
ZSCAN2 ENST00000448803 51.74 44.18 46.65 0.58 0.62 0.66 1.82 1.95 1.87
RPL18A ENST00000222247 51.75 8.35 28.24 0.58 2.52 0.81 1.82 0.46 1.29
IRF2BP2 ENST00000366609 51.75 21.85 34.98 0.58 1.47 0.90 1.82 0.81 1.74
DCAF12L1 ENST00000371126 51.76 12.30 30.21 0.58 2.06 0.81 1.82 0.59 1.44
E2F5 ENST00000416274 51.76 17.45 32.79 0.58 1.58 0.85 1.82 0.74 1.64
SLC13A5 ENST00000433363 51.77 34.71 41.47 0.58 0.80 0.73 1.82 1.54 2.02
EAF2 ENST00000273668 51.77 78.23 66.73 0.58 0.43 0.54 1.82 0.74 1.20
TUB ENST00000305253 51.78 29.48 38.96 0.58 1.10 0.80 1.82 1.39 2.06

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