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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
C3orf80 ENST00000326474 90.26 83.69 90.19 0.16 0.27 0.18 0.26 0.47 0.21
SMIM1 ENST00000444870 90.27 90.23 93.12 0.16 0.25 0.14 0.26 0.38 0.15
C19orf82 ENST00000587536 90.27 90.77 93.35 0.16 0.25 0.13 0.26 0.35 0.15
AC018755.1 ENST00000301439 90.28 78.98 87.87 0.16 0.40 0.24 0.26 0.69 0.32
FOXI2 ENST00000388920 90.28 91.87 94.06 0.16 0.23 0.09 0.26 0.32 0.12
ANKRD66 ENST00000565422 90.29 89.84 94.42 0.16 0.27 0.10 0.26 0.37 0.12
APLN ENST00000307484 90.29 80.62 88.81 0.16 0.37 0.19 0.26 0.57 0.28
DEFB114 ENST00000322066 90.30 93.56 94.95 0.15 0.28 0.09 0.26 0.28 0.10
SULT1A4 ENST00000395400 90.31 88.20 92.07 0.15 0.23 0.14 0.25 0.38 0.16
RP11-650K20.3 ENST00000551650 90.31 79.41 88.13 0.15 0.38 0.23 0.25 0.67 0.30
CCDC152 ENST00000361970 90.32 69.70 83.49 0.15 0.53 0.33 0.25 1.12 0.40
CCDC85C ENST00000380243 90.32 23.66 56.99 0.15 1.40 0.49 0.25 0.93 1.70
RP13-996F3.4 ENST00000557886 90.33 95.74 95.90 0.15 0.23 0.07 0.25 0.20 0.10
TCF15 ENST00000246080 90.33 74.87 85.98 0.15 0.53 0.33 0.25 0.95 0.33
PRR15 ENST00000319694 90.34 68.37 82.88 0.15 0.52 0.32 0.25 1.21 0.40
SLX1B ENST00000330181 90.34 89.45 92.78 0.15 0.27 0.14 0.25 0.37 0.15
CCDC175 ENST00000537690 90.35 42.75 68.70 0.15 0.62 0.47 0.25 1.92 1.05
RNF187 ENST00000305943 90.35 63.63 80.46 0.15 0.49 0.39 0.25 1.23 0.50
AC106873.4 ENST00000420664 90.36 89.70 94.57 0.15 0.27 0.09 0.25 0.37 0.11
C16orf97 ENST00000562818 90.36 68.17 82.81 0.15 0.52 0.32 0.25 1.22 0.42
KRTAP20-4 ENST00000382828 90.37 97.89 97.07 0.15 0.21 0.08 0.25 0.17 0.07
KRTAP20-3 ENST00000382826 90.37 97.89 97.51 0.15 0.21 0.08 0.25 0.17 0.07
USP9Y ENST00000338981 90.38 29.98 60.94 0.15 1.09 0.43 0.25 1.41 1.57
AP000679.2 ENST00000319763 90.38 97.91 97.09 0.15 0.20 0.08 0.25 0.17 0.07
MEF2BNB ENST00000462790 90.39 62.22 79.77 0.15 0.53 0.38 0.25 1.34 0.53

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