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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
ADAM7 ENST00000175238 76.06 56.05 67.98 0.34 0.49 0.51 0.78 1.55 1.10
C1orf122 ENST00000373042 76.07 88.46 85.62 0.34 0.23 0.32 0.78 0.36 0.35
HIST1H2BF ENST00000359985 76.07 97.47 89.86 0.34 0.22 0.18 0.78 0.19 0.23
PLA2G10 ENST00000438167 76.08 95.37 88.80 0.34 0.24 0.19 0.78 0.21 0.28
SSTR4 ENST00000255008 76.08 97.23 89.74 0.34 0.24 0.18 0.78 0.19 0.23
PYCARD ENST00000247470 76.09 90.93 86.68 0.34 0.25 0.30 0.78 0.35 0.33
LCE1F ENST00000334371 76.09 93.60 88.02 0.34 0.28 0.24 0.78 0.28 0.31
ZNF286B ENST00000545289 76.10 58.21 69.27 0.34 0.54 0.43 0.78 1.44 0.98
EVA1A ENST00000233712 76.10 79.88 81.34 0.34 0.37 0.38 0.78 0.61 0.49
OR8D4 ENST00000321355 76.11 65.22 73.46 0.34 0.51 0.40 0.77 1.24 0.76
KRTAP5-5 ENST00000399676 76.11 73.21 77.86 0.34 0.54 0.38 0.77 1.02 0.54
RSPH1 ENST00000291536 76.12 54.24 66.89 0.34 0.62 0.53 0.77 1.70 1.20
FADS6 ENST00000310226 76.12 87.30 85.07 0.34 0.22 0.33 0.77 0.41 0.38
HDGFL1 ENST00000510882 76.13 45.05 61.28 0.34 0.67 0.44 0.77 1.97 1.48
PDZK1 ENST00000344770 76.13 87.72 85.27 0.34 0.24 0.34 0.77 0.37 0.36
SLC3A1 ENST00000260649 76.14 81.94 82.43 0.34 0.35 0.33 0.77 0.51 0.44
CCDC136 ENST00000297788 76.14 37.22 56.50 0.34 0.77 0.52 0.77 1.66 1.70
RGS9BP ENST00000334176 76.15 87.55 85.18 0.34 0.23 0.33 0.77 0.37 0.37
HIST1H4E ENST00000360441 76.15 96.18 89.27 0.34 0.22 0.19 0.77 0.20 0.25
CCR5 ENST00000343801 76.16 95.22 88.78 0.34 0.23 0.19 0.77 0.21 0.28
TNFAIP8L1 ENST00000536716 76.16 66.68 74.28 0.34 0.56 0.39 0.76 1.22 0.69
IFI35 ENST00000438323 76.17 73.61 78.11 0.34 0.52 0.39 0.76 1.03 0.55
FAM127C ENST00000391440 76.17 96.05 89.21 0.34 0.21 0.19 0.76 0.20 0.25
DHFRL1 ENST00000394221 76.18 84.37 83.68 0.34 0.29 0.33 0.76 0.44 0.40
TMEM192 ENST00000306480 76.18 75.37 79.09 0.34 0.47 0.39 0.76 0.89 0.53

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