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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
FAM183B ENST00000409072 94.34 99.63 98.29 0.10 0.16 0.09 0.11 0.12 0.05
KRTAP4-3 ENST00000391356 89.57 99.63 96.64 0.16 0.16 0.08 0.30 0.12 0.08
AC013449.1 ENST00000599234 80.82 99.64 92.91 0.32 0.17 0.14 0.60 0.12 0.15
USP29 ENST00000254181 94.94 99.64 98.76 0.10 0.17 0.10 0.12 0.12 0.05
KRTAP19-5 ENST00000334151 85.64 99.65 95.43 0.28 0.17 0.08 0.46 0.12 0.11
ZNF491 ENST00000323169 96.62 99.65 99.58 0.11 0.17 0.12 0.11 0.12 0.05
PYDC2 ENST00000518817 94.59 99.66 99.07 0.10 0.17 0.11 0.12 0.12 0.04
AP003062.1 ENST00000597621 89.16 99.66 97.18 0.19 0.17 0.08 0.32 0.12 0.06
AL020996.1 ENST00000536896 93.66 99.67 98.81 0.13 0.17 0.10 0.13 0.12 0.05
AC024940.1 ENST00000313737 93.69 99.67 98.82 0.13 0.17 0.10 0.13 0.12 0.05
AC079210.1 ENST00000600820 75.17 99.68 90.08 0.38 0.17 0.18 0.76 0.12 0.22
PSAPL1 ENST00000319098 97.21 99.28 99.61 0.10 0.15 0.12 0.11 0.12 0.05
DCAF8L1 ENST00000441525 84.26 99.28 94.56 0.30 0.15 0.09 0.47 0.12 0.11
MTRNR2L2 ENST00000604882 92.89 99.29 98.22 0.15 0.15 0.09 0.16 0.12 0.05
TBC1D3G ENST00000341264 92.92 99.29 98.52 0.16 0.16 0.10 0.16 0.12 0.05
AL391152.1 ENST00000391612 92.92 99.30 98.53 0.16 0.16 0.10 0.16 0.12 0.05
KRTAP12-1 ENST00000391617 83.67 99.30 94.33 0.29 0.16 0.10 0.52 0.12 0.12
KRTAP12-4 ENST00000391618 98.04 99.31 99.79 0.11 0.16 0.12 0.11 0.12 0.04
MRGPRE ENST00000436689 88.26 99.31 96.34 0.20 0.16 0.07 0.35 0.12 0.09
C22orf29 ENST00000405640 95.55 99.32 99.25 0.11 0.16 0.11 0.11 0.12 0.04
MAGEC2 ENST00000247452 96.65 99.32 99.52 0.11 0.16 0.12 0.11 0.12 0.05
TMEM78 ENST00000323223 92.97 99.33 98.55 0.16 0.16 0.10 0.16 0.12 0.05
ZFP42 ENST00000326866 96.32 99.33 99.43 0.12 0.16 0.11 0.11 0.12 0.05
KRTAP19-6 ENST00000334046 96.04 99.34 99.37 0.11 0.16 0.11 0.11 0.12 0.04
FAM217B ENST00000358293 80.70 99.34 92.85 0.32 0.16 0.14 0.57 0.12 0.15

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