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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
TBX22 ENST00000373294 64.44 11.79 36.25 0.56 2.09 0.85 1.20 0.57 1.84
FFAR1 ENST00000246553 64.44 83.05 76.89 0.56 0.30 0.35 1.20 0.49 0.60
TAF9B ENST00000341864 64.45 94.83 82.99 0.56 0.23 0.32 1.20 0.24 0.40
MBOAT4 ENST00000320542 64.45 64.13 65.91 0.56 0.49 0.51 1.20 1.21 1.24
ID3 ENST00000374561 64.46 37.28 49.82 0.56 0.76 0.65 1.20 1.66 1.90
SULT2B1 ENST00000201586 64.46 28.88 45.38 0.56 1.15 0.70 1.20 1.30 2.00
GCNT3 ENST00000396065 64.47 76.52 73.27 0.56 0.42 0.43 1.19 0.83 0.79
PNMT ENST00000269582 64.47 54.81 60.07 0.56 0.57 0.47 1.19 1.63 1.61
CCL3 ENST00000225245 64.48 56.82 61.32 0.56 0.54 0.44 1.19 1.54 1.48
PKHD1L1 ENST00000378402 64.49 56.35 61.01 0.56 0.52 0.43 1.19 1.53 1.56
ZDHHC20 ENST00000382466 64.49 36.66 49.51 0.56 0.77 0.67 1.19 1.66 1.84
OTUD6A ENST00000338352 64.50 93.70 82.52 0.56 0.28 0.33 1.19 0.27 0.43
ZNF502 ENST00000296091 64.50 60.64 63.84 0.56 0.53 0.49 1.19 1.41 1.39
ZNF518B ENST00000326756 64.51 28.98 45.45 0.56 1.15 0.70 1.19 1.31 1.99
EIF4EBP3 ENST00000310331 64.51 90.15 80.64 0.56 0.25 0.39 1.19 0.38 0.51
GCOM1 ENST00000380569 64.52 65.48 66.72 0.56 0.54 0.54 1.18 1.24 1.20
MBP ENST00000397860 64.52 41.11 52.06 0.56 0.59 0.61 1.18 1.82 1.93
CCT6B ENST00000314144 64.53 62.34 64.81 0.56 0.53 0.51 1.18 1.33 1.32
C14orf2 ENST00000414262 64.53 28.79 45.36 0.56 1.14 0.70 1.18 1.29 2.00
GPKOW ENST00000156109 64.54 5.05 32.95 0.56 3.21 0.86 1.18 0.32 1.67
EVPL ENST00000301607 64.54 40.29 51.57 0.56 0.62 0.62 1.18 1.74 1.94
LARP7 ENST00000509061 64.55 47.84 55.86 0.56 0.59 0.51 1.18 1.98 1.75
C7orf31 ENST00000409280 64.55 56.12 60.95 0.56 0.52 0.43 1.18 1.56 1.58
HLX ENST00000366903 64.56 18.55 39.90 0.56 1.49 0.78 1.18 0.76 2.02
COX4I2 ENST00000376075 64.56 72.16 70.70 0.56 0.52 0.43 1.18 1.04 0.87

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