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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
GMPR ENST00000259727 64.18 56.87 61.13 0.57 0.56 0.43 1.20 1.53 1.51
GAS1 ENST00000298743 64.19 28.01 44.67 0.57 1.20 0.62 1.19 1.18 2.06
OLFM4 ENST00000219022 64.19 56.32 60.88 0.57 0.52 0.43 1.19 1.55 1.59
SLC26A8 ENST00000490799 64.20 45.40 54.35 0.57 0.68 0.59 1.19 2.01 1.74
SLC25A23 ENST00000301454 64.20 30.37 45.98 0.57 1.08 0.70 1.19 1.39 1.97
TRAPPC2L ENST00000301021 64.21 96.17 83.59 0.57 0.21 0.33 1.19 0.20 0.40
GRXCR2 ENST00000377976 64.21 82.08 76.23 0.57 0.34 0.37 1.19 0.51 0.62
ZNF862 ENST00000223210 64.22 46.41 54.86 0.57 0.73 0.51 1.19 2.04 1.74
MTFMT ENST00000220058 64.22 49.07 56.46 0.57 0.67 0.52 1.19 2.03 1.70
C3orf84 ENST00000545770 64.23 76.40 73.04 0.57 0.43 0.42 1.19 0.86 0.80
KRT81 ENST00000327741 64.23 93.99 82.53 0.57 0.25 0.32 1.19 0.26 0.43
ENTHD1 ENST00000325157 64.24 57.11 61.34 0.57 0.56 0.44 1.19 1.49 1.48
PPP1R14D ENST00000427255 64.24 82.70 76.57 0.57 0.34 0.37 1.19 0.50 0.61
HELB ENST00000247815 64.25 63.75 65.56 0.57 0.49 0.52 1.19 1.22 1.30
MAATS1 ENST00000273390 64.25 50.26 57.17 0.57 0.67 0.52 1.19 1.99 1.69
TRAPPC12 ENST00000324266 64.26 64.41 65.94 0.57 0.48 0.51 1.19 1.22 1.23
NR1I2 ENST00000337940 64.26 65.87 66.78 0.56 0.54 0.53 1.19 1.23 1.20
CRYGC ENST00000282141 64.27 71.64 70.18 0.56 0.53 0.43 1.19 1.07 0.91
EPB41L4A ENST00000261486 64.27 55.66 60.50 0.56 0.52 0.44 1.19 1.60 1.58
TM2D1 ENST00000371180 64.28 63.32 65.27 0.56 0.47 0.53 1.19 1.31 1.31
SSNA1 ENST00000322310 64.28 90.18 80.55 0.56 0.25 0.39 1.19 0.38 0.51
CRYZ ENST00000417775 64.29 95.39 83.21 0.56 0.24 0.29 1.19 0.21 0.40
ZC2HC1C ENST00000524913 64.29 71.76 70.32 0.56 0.51 0.43 1.18 1.07 0.90
MDC1 ENST00000376406 64.30 27.79 44.60 0.56 1.23 0.62 1.18 1.18 2.05
GPR132 ENST00000329797 64.30 76.81 73.34 0.56 0.42 0.43 1.19 0.81 0.78

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