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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
RP4-758J18.2 ENST00000448629 91.17 86.90 93.10 0.15 0.22 0.14 0.21 0.41 0.15
AL353698.1 ENST00000433279 91.17 98.27 97.62 0.15 0.21 0.09 0.21 0.15 0.06
AC079341.1 ENST00000424958 91.18 98.28 97.65 0.15 0.21 0.09 0.21 0.15 0.06
RBMY1A1 ENST00000382707 91.18 93.58 95.36 0.15 0.28 0.08 0.21 0.28 0.10
RP11-536G4.1 ENST00000553095 91.19 94.32 95.98 0.15 0.24 0.07 0.21 0.25 0.10
CTC-241N9.1 ENST00000499601 91.19 98.30 97.67 0.15 0.21 0.09 0.21 0.14 0.06
AL033381.1 ENST00000314040 91.20 96.19 96.98 0.15 0.22 0.08 0.21 0.20 0.07
C9orf16 ENST00000372994 91.20 95.09 96.12 0.15 0.23 0.07 0.21 0.21 0.10
C17orf89 ENST00000431388 91.21 88.12 92.64 0.15 0.24 0.14 0.21 0.38 0.15
KDM5D ENST00000317961 91.21 15.41 53.37 0.15 1.89 0.62 0.21 0.67 1.85
C19orf24 ENST00000409293 91.22 96.21 96.75 0.15 0.22 0.08 0.21 0.20 0.08
TMEM238 ENST00000444469 91.22 93.27 95.22 0.15 0.28 0.08 0.21 0.30 0.10
RP11-219B4.5 ENST00000546501 91.23 96.12 96.68 0.15 0.21 0.08 0.21 0.20 0.08
LRRC70 ENST00000334994 91.23 61.72 80.42 0.15 0.57 0.38 0.21 1.38 0.50
CEBPD ENST00000408965 91.24 55.96 75.91 0.15 0.49 0.38 0.21 1.56 0.62
BBC3 ENST00000449228 91.25 85.64 91.30 0.15 0.27 0.15 0.21 0.44 0.18
TEN1 ENST00000397640 91.25 75.98 87.05 0.15 0.43 0.28 0.21 0.86 0.30
GOLGA8F ENST00000532622 91.26 78.74 88.53 0.15 0.42 0.22 0.21 0.73 0.28
AC007421.1 ENST00000593717 91.26 98.32 98.60 0.15 0.21 0.10 0.21 0.14 0.05
C12orf75 ENST00000443585 91.27 49.93 73.86 0.15 0.66 0.42 0.20 2.02 0.71
CTD-2021H9.3 ENST00000549357 91.27 93.34 95.25 0.15 0.28 0.08 0.20 0.29 0.10
CKS1B ENST00000600888 91.28 98.34 97.72 0.15 0.21 0.09 0.20 0.14 0.05
FLJ00104 ENST00000446344 91.28 98.35 97.74 0.15 0.21 0.09 0.20 0.14 0.05
GAGE2D ENST00000404720 91.29 84.07 90.44 0.15 0.27 0.15 0.20 0.45 0.21
HIST1H4J ENST00000355057 91.29 87.61 92.37 0.15 0.23 0.14 0.20 0.36 0.15

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