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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
BCL9 ENST00000234739 36.42 17.93 25.26 0.95 1.54 1.05 1.81 0.73 1.15
ST3GAL5 ENST00000377332 36.42 39.14 35.89 0.95 0.70 0.86 1.81 1.62 1.79
MCMDC2 ENST00000422365 36.43 49.28 41.06 0.95 0.65 0.75 1.81 2.02 2.06
KANK4 ENST00000371153 36.43 43.07 38.02 0.95 0.61 0.85 1.81 1.90 2.02
SMG9 ENST00000270066 36.44 58.33 46.08 0.95 0.54 0.68 1.81 1.41 1.97
CAP2 ENST00000229922 36.44 19.33 26.06 0.95 1.48 0.99 1.80 0.74 1.25
STARD13 ENST00000336934 36.45 33.22 32.98 0.95 0.82 0.86 1.80 1.49 1.67
NKAIN3 ENST00000523211 36.45 39.10 35.89 0.95 0.70 0.86 1.80 1.63 1.79
PRMT2 ENST00000397637 36.46 30.94 31.90 0.95 1.05 0.91 1.80 1.35 1.57
HSPB2 ENST00000304298 36.47 77.06 56.58 0.95 0.42 0.52 1.80 0.78 1.70
RPP40 ENST00000380051 36.47 49.54 41.21 0.95 0.66 0.76 1.80 2.04 2.02
MYO1E ENST00000288235 36.48 22.05 27.40 0.95 1.48 0.96 1.80 0.81 1.27
KRT222 ENST00000394052 36.48 57.02 45.46 0.95 0.56 0.70 1.79 1.51 1.97
C16orf52 ENST00000542527 36.49 51.36 42.19 0.95 0.63 0.68 1.78 1.89 2.01
NSMAF ENST00000427130 36.49 35.24 34.05 0.95 0.76 0.91 1.78 1.58 1.73
WNT5A ENST00000474267 36.50 10.13 21.43 0.95 2.33 1.32 1.78 0.49 0.91
RIT2 ENST00000326695 36.50 74.51 55.09 0.95 0.53 0.51 1.78 1.00 1.73
GLRX3 ENST00000368644 36.51 24.79 28.78 0.95 1.32 0.80 1.78 1.05 1.32
IDS ENST00000422081 36.51 14.42 23.56 0.95 2.06 1.19 1.78 0.61 1.01
TM4SF19 ENST00000273695 36.52 80.77 58.76 0.95 0.37 0.52 1.78 0.57 1.65
UTP14A ENST00000394422 36.52 3.41 17.90 0.95 3.42 1.68 1.78 0.29 0.77
NDUFV2 ENST00000318388 36.53 45.73 39.47 0.95 0.75 0.78 1.78 2.02 2.04
SNCAIP ENST00000261368 36.53 26.73 29.82 0.95 1.20 0.86 1.78 1.12 1.43
CBX4 ENST00000269397 36.54 11.14 21.98 0.95 2.09 1.19 1.78 0.54 0.96
UHRF1BP1 ENST00000192788 36.54 33.04 32.96 0.95 0.85 0.86 1.78 1.49 1.67

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