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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
GSG2 ENST00000325418 70.64 54.26 63.64 0.49 0.62 0.49 0.91 1.70 1.38
LMAN1L ENST00000309664 70.64 65.80 70.52 0.49 0.54 0.43 0.91 1.22 0.91
ZNF205 ENST00000382192 70.65 29.45 48.94 0.49 1.09 0.71 0.91 1.38 1.84
OR51F1 ENST00000343430 70.65 70.05 73.09 0.49 0.53 0.42 0.91 1.14 0.80
OBSL1 ENST00000404537 70.66 46.63 58.75 0.49 0.75 0.52 0.91 1.99 1.65
MTRF1L ENST00000367233 70.66 79.13 78.12 0.49 0.39 0.39 0.91 0.69 0.55
CD101 ENST00000256652 70.67 46.04 58.37 0.49 0.77 0.49 0.91 2.04 1.65
ELMOD3 ENST00000315658 70.67 82.37 79.85 0.49 0.34 0.37 0.91 0.52 0.52
ATP6V1E2 ENST00000306448 70.68 66.30 70.83 0.49 0.54 0.43 0.91 1.20 0.86
KIF18B ENST00000593135 70.68 27.85 48.12 0.49 1.23 0.66 0.91 1.19 1.87
NCF4 ENST00000397147 70.69 66.56 71.02 0.49 0.56 0.43 0.91 1.21 0.85
SRPX ENST00000378533 70.69 41.77 55.91 0.49 0.61 0.49 0.91 1.78 1.76
CCDC141 ENST00000420890 70.70 51.89 62.07 0.49 0.59 0.48 0.91 1.86 1.45
GPR146 ENST00000397095 70.70 56.36 64.97 0.49 0.52 0.51 0.90 1.53 1.32
SPATA18 ENST00000295213 70.71 60.23 67.25 0.49 0.53 0.52 0.90 1.39 1.16
NOX5 ENST00000388866 70.71 78.06 77.61 0.49 0.43 0.38 0.90 0.76 0.56
C14orf37 ENST00000267485 70.72 47.40 59.27 0.49 0.66 0.51 0.90 2.01 1.68
FAM127B ENST00000370775 70.72 81.97 79.59 0.49 0.35 0.38 0.90 0.50 0.52
C16orf11 ENST00000409413 70.73 55.52 64.40 0.49 0.56 0.51 0.90 1.60 1.34
SLC14A1 ENST00000436407 70.73 77.50 77.28 0.49 0.42 0.35 0.90 0.78 0.58
SLC16A3 ENST00000581287 70.74 63.26 69.08 0.49 0.47 0.44 0.90 1.31 1.01
FSD2 ENST00000334574 70.75 70.19 73.21 0.49 0.53 0.43 0.90 1.12 0.79
OR56A1 ENST00000316650 70.75 86.62 82.06 0.49 0.24 0.35 0.90 0.40 0.46
RRAS ENST00000246792 70.76 61.43 68.02 0.49 0.54 0.51 0.90 1.39 1.10
PXMP2 ENST00000317479 70.76 69.60 72.94 0.49 0.52 0.40 0.90 1.10 0.81

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