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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
NUTM1 ENST00000333756 65.99 28.11 45.75 0.59 1.19 0.68 1.05 1.20 1.98
OR9I1 ENST00000302610 65.99 53.34 60.10 0.59 0.66 0.48 1.05 1.70 1.61
MARCKSL1 ENST00000329421 66.00 83.82 78.15 0.59 0.27 0.39 1.05 0.47 0.55
IQCK ENST00000320394 66.00 63.02 66.17 0.59 0.48 0.52 1.05 1.31 1.20
CLDN6 ENST00000396925 66.01 83.95 78.25 0.59 0.28 0.37 1.05 0.46 0.55
PNKP ENST00000322344 66.01 71.53 71.23 0.59 0.53 0.44 1.05 1.07 0.86
GSDMA ENST00000301659 66.02 76.33 73.99 0.59 0.43 0.39 1.05 0.85 0.70
GDF3 ENST00000329913 66.02 70.38 70.50 0.59 0.52 0.43 1.05 1.08 0.91
SDCBP2 ENST00000360779 66.03 76.34 73.97 0.59 0.43 0.39 1.05 0.85 0.69
FOXK2 ENST00000335255 66.03 22.48 42.51 0.59 1.51 0.68 1.05 0.84 2.01
DDI1 ENST00000302259 66.04 83.07 77.76 0.59 0.30 0.38 1.05 0.49 0.55
ZNF511 ENST00000361518 66.05 72.22 71.70 0.59 0.51 0.46 1.05 1.04 0.82
PCDHB4 ENST00000194152 66.05 74.43 72.99 0.59 0.53 0.40 1.05 1.00 0.80
DMRT2 ENST00000382251 66.06 39.42 51.92 0.59 0.70 0.62 1.05 1.64 1.94
PARPBP ENST00000358383 66.06 74.75 73.14 0.59 0.54 0.43 1.05 0.96 0.79
PCNXL4 ENST00000317623 66.07 65.83 67.85 0.59 0.54 0.51 1.05 1.22 1.11
CREG2 ENST00000324768 66.07 84.47 78.50 0.59 0.29 0.38 1.05 0.44 0.55
CDKN1B ENST00000228872 66.08 31.73 47.72 0.59 0.95 0.65 1.05 1.47 1.88
LRRC48 ENST00000313838 66.08 52.02 59.27 0.59 0.61 0.51 1.05 1.86 1.68
COX14 ENST00000550487 66.09 89.28 81.04 0.59 0.27 0.39 1.06 0.37 0.49
GLRX2 ENST00000367440 66.09 83.93 78.28 0.59 0.28 0.38 1.06 0.47 0.55
PKP2 ENST00000070846 66.10 57.54 62.77 0.59 0.57 0.48 1.06 1.48 1.39
SAFB2 ENST00000252542 66.10 7.93 35.19 0.59 2.54 0.86 1.07 0.44 1.75
CENPF ENST00000366955 66.11 38.68 51.54 0.59 0.70 0.62 1.07 1.66 1.92
HELT ENST00000338875 66.11 50.40 58.30 0.59 0.66 0.49 1.07 1.95 1.65

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