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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
BPIFC ENST00000397452 60.69 45.99 52.67 0.57 0.77 0.59 1.33 2.02 1.90
LIMS2 ENST00000324938 61.07 48.49 54.31 0.59 0.65 0.59 1.34 2.02 1.73
ZNF311 ENST00000377179 61.11 46.54 53.26 0.62 0.75 0.61 1.33 2.02 1.87
C3orf17 ENST00000314400 61.28 49.87 55.16 0.65 0.66 0.51 1.32 2.02 1.74
F3 ENST00000334047 61.36 45.80 52.96 0.66 0.75 0.61 1.34 2.02 1.87
C11orf82 ENST00000533655 61.71 47.44 54.08 0.71 0.65 0.59 1.29 2.02 1.76
MRPL39 ENST00000307301 63.10 49.88 56.24 0.59 0.66 0.49 1.26 2.02 1.76
VWA3A ENST00000389398 64.04 49.86 56.78 0.57 0.66 0.52 1.20 2.02 1.70
C2orf43 ENST00000237822 64.06 49.29 56.51 0.57 0.65 0.52 1.19 2.02 1.70
ZP3 ENST00000394857 66.69 49.34 58.07 0.62 0.65 0.47 1.05 2.02 1.66
HHATL ENST00000441594 66.86 47.44 57.02 0.59 0.65 0.51 1.04 2.02 1.70
KNG1 ENST00000265023 68.94 49.94 59.75 0.57 0.66 0.49 0.95 2.02 1.66
PRKX ENST00000262848 69.20 49.93 59.99 0.57 0.66 0.48 0.97 2.02 1.63
EXPH5 ENST00000265843 70.83 49.85 60.97 0.47 0.66 0.43 0.89 2.02 1.58
POC5 ENST00000428202 72.33 49.33 61.55 0.34 0.65 0.46 0.80 2.02 1.48
DLGAP5 ENST00000247191 75.60 49.32 63.67 0.34 0.65 0.49 0.75 2.02 1.39
LIPE ENST00000244289 76.93 47.47 63.29 0.33 0.63 0.49 0.73 2.02 1.36
HIRIP3 ENST00000279392 77.14 49.60 64.76 0.34 0.66 0.49 0.72 2.02 1.32
SH2B3 ENST00000341259 78.11 45.81 63.03 0.34 0.75 0.51 0.66 2.02 1.39
CARS2 ENST00000257347 78.16 45.70 62.96 0.34 0.75 0.51 0.66 2.02 1.39
ZNF175 ENST00000262259 78.32 49.46 65.45 0.35 0.66 0.52 0.66 2.02 1.31
AGPAT5 ENST00000285518 78.74 46.49 63.88 0.35 0.73 0.49 0.65 2.02 1.39
FAM21C ENST00000374362 78.85 45.71 63.47 0.33 0.75 0.49 0.65 2.02 1.38
ZNF350 ENST00000243644 80.29 45.74 64.29 0.32 0.75 0.51 0.57 2.02 1.35
C6orf132 ENST00000341865 85.03 47.52 68.27 0.28 0.62 0.52 0.46 2.02 1.07

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