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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
GLRA4 ENST00000372617 46.10 75.96 61.77 0.58 0.43 0.46 1.81 0.86 1.47
C11orf87 ENST00000327419 46.11 68.46 57.19 0.58 0.52 0.52 1.81 1.20 1.70
LOXL1 ENST00000261921 46.11 17.84 30.16 0.58 1.51 0.81 1.81 0.72 1.46
ZNF407 ENST00000299687 46.12 0.88 21.66 0.58 4.09 1.27 1.81 0.29 0.91
PSMD8 ENST00000215071 46.12 32.18 37.41 0.58 0.87 0.85 1.81 1.46 2.00
CYB561 ENST00000392976 46.13 33.31 38.00 0.58 0.84 0.85 1.81 1.51 2.03
ABCC10 ENST00000372530 46.13 54.13 49.00 0.58 0.63 0.72 1.81 1.68 1.84
TDRD9 ENST00000409874 46.14 33.12 37.86 0.58 0.82 0.85 1.81 1.50 2.01
CACNA1S ENST00000362061 46.14 27.15 34.83 0.58 1.24 0.90 1.81 1.14 1.76
PDZD2 ENST00000438447 46.15 11.34 26.91 0.58 2.11 0.97 1.81 0.56 1.27
PEX19 ENST00000368072 46.15 51.26 47.50 0.58 0.65 0.63 1.81 1.90 1.89
PFAS ENST00000314666 46.16 41.59 42.11 0.58 0.63 0.71 1.81 1.80 1.99
C1QL4 ENST00000334221 46.16 47.21 45.37 0.57 0.66 0.70 1.81 2.01 2.00
TSPO2 ENST00000373161 46.17 85.61 67.76 0.57 0.27 0.52 1.81 0.44 1.12
APOBEC2 ENST00000244669 46.18 56.75 50.51 0.57 0.53 0.67 1.80 1.55 1.86
NCKIPSD ENST00000294129 46.18 30.68 36.53 0.56 1.05 0.85 1.80 1.38 1.90
TRPM8 ENST00000324695 46.19 58.15 51.30 0.56 0.54 0.63 1.80 1.45 1.92
BCR ENST00000305877 46.19 10.58 26.49 0.54 2.15 0.99 1.80 0.51 1.25
AGBL2 ENST00000525123 46.20 48.44 46.04 0.54 0.63 0.68 1.80 2.02 1.97
PLD1 ENST00000351298 46.20 47.13 45.35 0.54 0.66 0.70 1.80 2.01 1.99
GALNS ENST00000268695 46.21 54.14 49.09 0.54 0.63 0.72 1.80 1.68 1.82
DUOXA1 ENST00000267803 46.21 57.57 50.96 0.56 0.57 0.66 1.80 1.47 1.85
ARHGDIB ENST00000228945 46.22 69.59 57.94 0.56 0.52 0.48 1.80 1.10 1.66
PFKFB4 ENST00000232375 46.22 53.72 48.87 0.56 0.63 0.71 1.80 1.70 1.85
TWF2 ENST00000305533 46.23 12.92 27.73 0.56 2.07 0.92 1.79 0.59 1.27

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