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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
TENM1 ENST00000422452 21.57 5.33 11.10 1.56 3.11 2.19 1.06 0.32 0.45
RFT1 ENST00000296292 21.57 59.54 38.88 1.56 0.49 0.80 1.06 1.40 2.05
NMT2 ENST00000378165 21.58 21.69 19.64 1.56 1.46 1.53 1.06 0.81 0.85
NAGS ENST00000293404 21.58 62.31 40.21 1.56 0.53 0.82 1.06 1.33 2.00
ZGLP1 ENST00000403903 21.59 35.22 26.51 1.56 0.76 0.99 1.06 1.58 1.25
CHAMP1 ENST00000361283 21.59 10.03 13.41 1.56 2.35 2.05 1.05 0.49 0.55
SLC16A10 ENST00000368851 21.60 27.89 22.91 1.56 1.21 1.19 1.05 1.18 0.97
RAPGEF6 ENST00000296859 21.61 11.06 14.02 1.56 2.09 2.04 1.05 0.52 0.60
SCN5A ENST00000413689 21.61 13.27 15.20 1.56 2.05 1.83 1.06 0.60 0.64
ADCY6 ENST00000307885 21.62 22.18 19.92 1.56 1.53 1.46 1.06 0.81 0.85
COCH ENST00000396618 21.62 48.37 33.15 1.56 0.63 0.87 1.06 2.00 1.68
GLTSCR1 ENST00000396720 21.63 12.82 15.04 1.56 2.09 1.87 1.06 0.59 0.63
ARHGDIA ENST00000269321 21.63 52.04 35.02 1.56 0.61 0.87 1.06 1.86 1.73
PCDH19 ENST00000373034 21.64 2.21 9.38 1.56 3.65 2.29 1.06 0.30 0.39
SLC7A5 ENST00000261622 21.64 26.52 22.21 1.54 1.19 1.15 1.06 1.12 0.96
DOCK11 ENST00000276202 21.65 16.31 16.82 1.56 1.78 1.70 1.06 0.70 0.69
KIAA2013 ENST00000376572 21.65 40.28 29.14 1.56 0.61 0.84 1.06 1.75 1.32
NNT ENST00000264663 21.66 11.66 14.39 1.56 2.09 2.01 1.06 0.57 0.59
HTR1E ENST00000305344 21.66 40.68 29.36 1.56 0.63 0.82 1.05 1.78 1.35
SLAIN2 ENST00000264313 21.67 20.06 18.86 1.56 1.43 1.56 1.05 0.74 0.83
FTH1 ENST00000273550 21.67 39.79 28.86 1.54 0.65 0.82 1.05 1.67 1.31
PAX9 ENST00000361487 21.68 32.23 24.99 1.54 0.86 1.02 1.05 1.46 1.14
FXYD6-FXYD2 ENST00000532984 21.68 22.03 19.90 1.54 1.48 1.46 1.05 0.81 0.85
PIK3AP1 ENST00000339364 21.69 1.96 9.28 1.54 3.75 2.32 1.05 0.25 0.38
USP42 ENST00000306177 21.69 2.32 9.43 1.54 3.63 2.29 1.05 0.29 0.40

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