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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
LRRC37A2 ENST00000576629 97.49 46.30 74.81 0.10 0.73 0.39 0.11 2.05 0.66
ZDHHC11 ENST00000283441 97.50 80.85 91.94 0.10 0.35 0.14 0.11 0.57 0.16
MAGEB6 ENST00000379034 97.51 98.03 99.40 0.10 0.20 0.11 0.11 0.16 0.04
C22orf43 ENST00000317749 97.51 86.30 94.64 0.10 0.25 0.09 0.11 0.43 0.11
RPA4 ENST00000373040 97.52 98.86 99.61 0.10 0.16 0.12 0.11 0.14 0.05
ZNF426 ENST00000535489 97.52 75.09 89.42 0.10 0.51 0.18 0.11 0.91 0.24
NLRP1 ENST00000572272 97.53 43.68 73.38 0.10 0.62 0.42 0.11 1.97 0.78
HENMT1 ENST00000370032 97.53 79.44 91.38 0.10 0.38 0.15 0.11 0.66 0.18
PRKACG ENST00000377276 97.54 98.64 99.50 0.10 0.20 0.12 0.11 0.15 0.05
CMTM2 ENST00000268595 97.54 84.76 93.92 0.10 0.27 0.09 0.11 0.42 0.11
CSAG1 ENST00000370287 97.55 90.79 96.95 0.10 0.25 0.08 0.11 0.35 0.07
MRGPRD ENST00000309106 97.55 97.59 99.28 0.10 0.22 0.11 0.11 0.20 0.04
FCRL5 ENST00000361835 97.56 58.18 81.19 0.10 0.54 0.38 0.11 1.46 0.49
FAM71A ENST00000294829 97.56 97.68 99.31 0.10 0.21 0.11 0.11 0.19 0.04
CEACAM4 ENST00000221954 97.57 81.03 92.04 0.10 0.35 0.14 0.11 0.55 0.16
PYDC1 ENST00000302964 97.57 98.15 99.47 0.10 0.20 0.11 0.11 0.16 0.05
TCL1B ENST00000340722 97.58 75.25 89.54 0.10 0.49 0.18 0.11 0.90 0.23
PAGE1 ENST00000376150 97.58 34.00 67.62 0.10 0.84 0.51 0.11 1.55 1.13
ZNF493 ENST00000392288 97.59 93.40 97.98 0.10 0.28 0.09 0.11 0.28 0.04
RAET1L ENST00000367341 97.59 92.70 97.71 0.10 0.29 0.09 0.11 0.30 0.05
CRB3 ENST00000356762 97.60 55.79 80.03 0.10 0.52 0.35 0.11 1.58 0.52
ZNF616 ENST00000600228 97.60 90.31 96.75 0.10 0.25 0.08 0.11 0.38 0.08
TMEM176A ENST00000484928 97.61 51.43 77.72 0.10 0.63 0.38 0.11 1.89 0.55
ZNF814 ENST00000435989 97.61 86.24 94.66 0.10 0.27 0.09 0.11 0.43 0.11
NBPF4 ENST00000415641 97.62 83.63 93.34 0.10 0.27 0.13 0.11 0.47 0.15

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