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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
PEX7 ENST00000318471 32.54 75.21 53.29 0.96 0.49 0.61 1.70 0.91 1.86
TOR1A ENST00000351698 32.55 60.36 45.12 0.96 0.53 0.70 1.70 1.41 2.01
C10orf12 ENST00000286067 32.56 6.37 17.34 0.96 2.66 1.63 1.70 0.37 0.75
KIF16B ENST00000408042 32.56 44.45 36.64 0.96 0.62 0.84 1.70 1.98 1.93
SYAP1 ENST00000380155 32.57 15.68 22.28 0.96 1.87 1.16 1.70 0.68 0.96
AMELX ENST00000380712 32.57 49.62 39.42 0.96 0.66 0.78 1.70 2.02 2.04
SMYD5 ENST00000389501 32.58 26.69 27.80 0.96 1.19 0.90 1.70 1.12 1.27
SFRP4 ENST00000436072 32.58 52.96 40.99 0.96 0.63 0.76 1.70 1.78 2.04
HID1 ENST00000425042 32.59 21.51 25.10 0.96 1.42 1.05 1.69 0.80 1.17
CDK5RAP1 ENST00000346416 32.59 75.46 53.44 0.96 0.46 0.62 1.70 0.90 1.83
CPXM1 ENST00000380605 32.60 49.21 39.29 0.96 0.66 0.80 1.70 2.04 2.04
ATRIP ENST00000320211 32.60 33.51 31.26 0.96 0.85 0.86 1.70 1.53 1.56
MAML1 ENST00000292599 32.61 3.02 15.66 0.96 3.47 1.76 1.70 0.28 0.67
STAMBP ENST00000394070 32.61 40.88 34.93 0.96 0.61 0.90 1.70 1.78 1.77
ITPK1 ENST00000267615 32.62 8.30 18.40 0.96 2.53 1.64 1.70 0.45 0.81
SCN1B ENST00000415950 32.62 66.77 48.61 0.96 0.56 0.67 1.70 1.22 1.85
ASXL3 ENST00000269197 32.63 4.89 16.58 0.96 3.27 1.72 1.70 0.31 0.70
CLDN10 ENST00000299339 32.63 67.26 48.84 0.96 0.56 0.70 1.70 1.21 1.85
UCHL1 ENST00000284440 32.64 7.02 17.74 0.96 2.57 1.67 1.70 0.37 0.78
VSIG8 ENST00000368100 32.64 46.08 37.63 0.96 0.75 0.82 1.70 2.03 2.01
PWP1 ENST00000412830 32.65 54.74 41.91 0.96 0.58 0.68 1.71 1.64 2.01
VPS26A ENST00000373382 32.65 24.45 26.71 0.96 1.32 1.00 1.71 1.00 1.27
ATP13A1 ENST00000357324 32.66 12.15 20.54 0.96 2.09 1.48 1.71 0.57 0.89
SLC25A1 ENST00000215882 32.66 33.89 31.49 0.95 0.84 0.86 1.71 1.55 1.57
NUDT15 ENST00000258662 32.67 75.55 53.52 0.95 0.44 0.63 1.71 0.90 1.82

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