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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
PGRMC2 ENST00000520121 70.12 31.83 49.96 0.49 0.94 0.61 0.93 1.48 1.90
PARVB ENST00000406477 70.13 70.88 73.28 0.49 0.49 0.43 0.93 1.07 0.79
POU5F2 ENST00000510627 70.13 88.79 82.85 0.49 0.25 0.32 0.93 0.35 0.41
C1orf177 ENST00000371273 70.14 68.84 72.15 0.49 0.53 0.43 0.93 1.19 0.82
IGF2 ENST00000434045 70.14 61.65 67.80 0.49 0.54 0.51 0.93 1.39 1.12
CTSE ENST00000358184 70.15 83.44 80.14 0.49 0.27 0.35 0.93 0.47 0.53
TMEM26 ENST00000399298 70.15 73.19 74.60 0.49 0.54 0.40 0.92 1.02 0.68
KLK8 ENST00000391806 70.16 52.73 62.27 0.49 0.66 0.49 0.92 1.79 1.42
OR2C3 ENST00000366487 70.16 78.08 77.28 0.49 0.43 0.35 0.92 0.74 0.58
HYI ENST00000372425 70.17 87.70 82.29 0.49 0.24 0.34 0.91 0.37 0.45
HAGH ENST00000397356 70.17 54.80 63.68 0.49 0.57 0.49 0.91 1.63 1.40
RPL14 ENST00000396203 70.18 18.64 42.70 0.49 1.49 0.68 0.91 0.75 2.03
PCDH11Y ENST00000362095 70.18 83.26 80.04 0.49 0.28 0.35 0.91 0.47 0.52
OR51I1 ENST00000380211 70.19 82.55 79.64 0.49 0.34 0.38 0.91 0.51 0.53
RFX8 ENST00000428343 70.19 61.14 67.47 0.49 0.53 0.52 0.92 1.40 1.14
HGSNAT ENST00000379644 70.20 39.15 54.19 0.49 0.70 0.59 0.92 1.62 1.74
ARL11 ENST00000282026 70.20 93.10 85.01 0.49 0.28 0.33 0.92 0.30 0.39
PEG3 ENST00000326441 70.21 25.86 46.74 0.49 1.21 0.67 0.92 1.08 1.87
GSTM1 ENST00000309851 70.21 56.25 64.58 0.49 0.52 0.51 0.92 1.56 1.33
KIAA0319 ENST00000378214 70.22 53.63 62.92 0.49 0.63 0.51 0.92 1.70 1.40
IAH1 ENST00000497473 70.22 49.74 60.51 0.49 0.66 0.44 0.91 2.02 1.58
RGAG1 ENST00000465301 70.23 6.99 36.80 0.49 2.59 0.82 0.91 0.37 1.94
TIFAB ENST00000537858 70.23 96.23 86.43 0.49 0.22 0.30 0.91 0.19 0.32
APOLD1 ENST00000326765 70.24 89.99 83.47 0.49 0.25 0.33 0.91 0.37 0.40
PCDHA8 ENST00000531613 70.24 73.81 74.98 0.49 0.53 0.40 0.91 1.02 0.66

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