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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
PCYT1A ENST00000292823 11.88 45.93 27.08 1.64 0.76 0.99 0.59 2.02 1.27
GCLM ENST00000370238 11.89 6.75 6.72 1.64 2.67 2.99 0.59 0.37 0.32
KCNH5 ENST00000322893 11.90 21.85 14.61 1.63 1.47 1.97 0.59 0.81 0.59
MAP4K3 ENST00000263881 11.90 15.14 11.16 1.63 1.90 2.18 0.59 0.66 0.45
ZFX ENST00000379177 11.91 3.42 4.94 1.63 3.41 3.69 0.60 0.28 0.25
CORO1C ENST00000261401 11.91 6.23 6.38 1.63 2.73 3.07 0.60 0.36 0.32
PTGES3 ENST00000262033 11.92 8.44 7.56 1.64 2.52 2.75 0.60 0.46 0.33
ADAM9 ENST00000487273 11.92 19.74 13.44 1.64 1.43 2.05 0.60 0.74 0.57
RBM6 ENST00000266022 11.93 2.40 4.45 1.64 3.61 3.71 0.61 0.29 0.25
SLC4A7 ENST00000295736 11.93 16.00 11.63 1.63 1.86 2.21 0.61 0.68 0.46
FGG ENST00000336098 11.94 26.62 17.13 1.63 1.20 1.64 0.61 1.12 0.73
LMX1B ENST00000355497 11.94 19.03 13.06 1.63 1.51 2.10 0.61 0.76 0.52
RASGRF1 ENST00000419573 11.95 6.49 6.60 1.63 2.63 3.00 0.61 0.37 0.32
MAPK3 ENST00000263025 11.95 30.62 19.27 1.62 1.06 1.53 0.61 1.39 0.85
MPPED1 ENST00000417669 11.96 44.06 26.15 1.62 0.61 0.99 0.61 1.97 1.27
EIF3A ENST00000369144 11.96 2.18 4.33 1.62 3.67 3.74 0.61 0.29 0.24
TXNDC9 ENST00000264255 11.97 35.91 22.04 1.63 0.80 1.15 0.61 1.58 0.97
SLC40A1 ENST00000261024 11.97 11.47 9.16 1.63 2.11 2.33 0.61 0.57 0.38
ZFC3H1 ENST00000378743 11.98 3.40 4.96 1.63 3.42 3.69 0.61 0.29 0.25
KLHL10 ENST00000293303 11.98 12.66 9.84 1.63 2.10 2.30 0.61 0.58 0.40
IGF1 ENST00000307046 11.99 42.15 25.14 1.63 0.62 1.05 0.61 1.86 1.16
IPO9 ENST00000361565 11.99 8.09 7.41 1.63 2.52 2.80 0.61 0.44 0.34
SPRYD3 ENST00000301463 12.00 25.79 16.76 1.64 1.21 1.70 0.61 1.05 0.70
FGL2 ENST00000248598 12.00 53.28 30.89 1.64 0.66 0.80 0.61 1.73 1.49
UNK ENST00000589666 12.01 5.15 5.84 1.64 3.21 3.30 0.61 0.32 0.28

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