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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
POTEM ENST00000551509 96.59 75.20 89.02 0.11 0.49 0.19 0.11 0.91 0.26
TM4SF20 ENST00000304568 96.60 83.09 92.59 0.11 0.29 0.14 0.11 0.49 0.15
HAUS8 ENST00000253669 96.60 57.58 80.41 0.11 0.57 0.38 0.11 1.48 0.50
LRRC66 ENST00000343457 96.61 90.83 96.50 0.11 0.25 0.07 0.11 0.35 0.07
ZNF479 ENST00000331162 96.61 89.34 95.76 0.11 0.27 0.07 0.11 0.37 0.11
ESX1 ENST00000372588 96.62 40.55 70.97 0.11 0.63 0.43 0.11 1.77 0.85
ZNF491 ENST00000323169 96.62 99.65 99.58 0.11 0.17 0.12 0.11 0.12 0.05
AC008060.7 ENST00000401499 96.63 94.19 97.91 0.11 0.25 0.09 0.11 0.25 0.04
MAGEA4 ENST00000360243 96.63 99.03 99.19 0.11 0.15 0.11 0.11 0.15 0.04
ZNF443 ENST00000301547 96.64 89.24 95.69 0.11 0.27 0.07 0.11 0.36 0.11
LRRFIP1 ENST00000392000 96.64 35.41 67.94 0.11 0.77 0.51 0.11 1.55 1.10
MAGEC2 ENST00000247452 96.65 99.32 99.52 0.11 0.16 0.12 0.11 0.12 0.05
LILRB5 ENST00000449561 96.65 78.73 90.76 0.11 0.42 0.15 0.11 0.73 0.20
ZNF578 ENST00000421239 96.66 93.53 97.68 0.11 0.28 0.09 0.11 0.28 0.06
DEFA4 ENST00000297435 96.66 78.59 90.68 0.11 0.40 0.15 0.11 0.74 0.20
MDS2 ENST00000374555 96.67 60.53 81.98 0.11 0.52 0.37 0.11 1.41 0.47
KHDC1 ENST00000370384 96.67 89.22 95.73 0.11 0.27 0.07 0.11 0.36 0.11
DEFB1 ENST00000297439 96.68 89.19 95.71 0.11 0.27 0.07 0.11 0.36 0.11
ZNF506 ENST00000443905 96.68 84.83 93.49 0.11 0.27 0.11 0.11 0.42 0.15
DIRC1 ENST00000308100 96.69 99.86 99.44 0.11 0.17 0.11 0.11 0.11 0.05
BCL2L10 ENST00000260442 96.69 87.46 94.80 0.11 0.23 0.09 0.11 0.40 0.11
VSTM1 ENST00000338372 96.70 77.24 90.05 0.11 0.43 0.18 0.11 0.78 0.22
C7orf33 ENST00000307003 96.70 92.13 97.16 0.11 0.24 0.08 0.11 0.32 0.07
TMEM105 ENST00000332900 96.71 95.91 98.53 0.11 0.22 0.10 0.11 0.20 0.05
CLC ENST00000221804 96.72 89.21 95.74 0.11 0.27 0.07 0.11 0.36 0.11

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