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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
GPR149 ENST00000389740 58.11 62.45 60.89 0.57 0.53 0.43 1.54 1.31 1.59
TMPRSS4 ENST00000437212 58.12 58.05 58.17 0.57 0.53 0.48 1.54 1.45 1.65
ZNF7 ENST00000528372 58.12 47.51 52.04 0.56 0.62 0.62 1.54 2.01 1.94
SETD9 ENST00000285947 58.13 55.00 56.36 0.56 0.57 0.49 1.54 1.63 1.75
ABTB1 ENST00000232744 58.13 39.96 47.90 0.56 0.63 0.66 1.54 1.68 1.89
WRNIP1 ENST00000380773 58.14 28.90 41.75 0.56 1.15 0.72 1.54 1.31 2.00
ITIH3 ENST00000449956 58.14 47.72 52.16 0.56 0.61 0.61 1.54 1.99 1.90
TPD52L2 ENST00000217121 58.15 57.81 58.04 0.56 0.57 0.47 1.54 1.47 1.66
NUDCD2 ENST00000302764 58.15 67.14 63.94 0.56 0.54 0.51 1.54 1.22 1.39
DGCR6 ENST00000331444 58.16 88.44 76.39 0.56 0.23 0.37 1.54 0.37 0.61
SPAG17 ENST00000336338 58.16 32.63 43.75 0.57 0.85 0.61 1.54 1.47 2.02
HAUS3 ENST00000243706 58.17 59.61 58.99 0.57 0.52 0.48 1.53 1.41 1.65
CKAP2L ENST00000302450 58.17 31.01 42.91 0.57 1.04 0.67 1.53 1.36 1.99
ANO2 ENST00000327087 58.18 49.33 53.18 0.57 0.65 0.61 1.54 2.02 1.87
PSMF1 ENST00000335877 58.18 78.97 70.97 0.57 0.40 0.43 1.54 0.69 0.85
LRIG1 ENST00000273261 58.19 20.17 37.43 0.57 1.43 0.86 1.54 0.75 2.01
BPIFB3 ENST00000375494 58.19 71.19 66.41 0.57 0.52 0.52 1.54 1.06 1.20
CTNNBIP1 ENST00000377263 58.20 75.67 68.99 0.57 0.44 0.46 1.54 0.90 1.03
OMP ENST00000529803 58.20 90.17 77.36 0.57 0.25 0.35 1.54 0.38 0.58
GUCY2F ENST00000218006 58.21 53.17 55.25 0.57 0.66 0.51 1.54 1.75 1.74
PDPR ENST00000288050 58.21 33.32 44.25 0.57 0.85 0.61 1.53 1.51 2.05
XIRP2 ENST00000409195 58.22 49.76 53.43 0.57 0.66 0.62 1.53 2.03 1.83
DNAJC24 ENST00000465995 58.23 91.13 77.88 0.57 0.25 0.38 1.53 0.35 0.54
B4GALNT4 ENST00000329962 58.23 25.54 40.15 0.57 1.25 0.82 1.53 1.05 1.99
CACNA2D4 ENST00000382722 58.24 56.01 56.98 0.57 0.49 0.49 1.53 1.56 1.70

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