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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
PPP3CB ENST00000394829 1.92 1.12 0.38 4.28 4.01 4.78 0.24 0.28 0.18
AP2A1 ENST00000359032 12.66 1.22 4.21 1.68 4.01 3.77 0.66 0.27 0.24
FBRS ENST00000356166 72.96 1.19 35.28 0.32 4.01 0.86 0.79 0.28 1.76
PSMD2 ENST00000310118 9.17 1.16 2.65 2.28 4.01 4.00 0.47 0.28 0.23
ILF3 ENST00000449870 8.71 1.13 2.51 2.42 4.01 4.01 0.44 0.28 0.24
LMNB2 ENST00000325327 46.00 1.22 21.76 0.58 4.01 1.25 1.79 0.27 0.93
RFX7 ENST00000423270 19.35 1.16 7.61 1.56 4.01 2.73 0.96 0.28 0.33
MAPK8IP2 ENST00000329492 38.03 1.13 17.45 0.91 4.01 1.62 1.73 0.28 0.76
CACNA1C ENST00000347598 2.98 1.23 0.64 3.90 4.00 4.65 0.30 0.27 0.19
CARM1 ENST00000327064 2.47 1.14 0.51 4.10 4.00 4.71 0.27 0.28 0.17
IGF2BP3 ENST00000258729 20.92 1.23 8.45 1.54 4.00 2.52 1.02 0.27 0.38
RPTOR ENST00000306801 5.88 1.14 1.52 3.15 4.00 4.33 0.33 0.28 0.22
CACNA1A ENST00000360228 6.06 1.24 1.61 3.05 4.00 4.27 0.34 0.27 0.23
PAXIP1 ENST00000404141 24.78 1.15 10.55 1.39 4.00 2.18 1.12 0.28 0.43
GAPVD1 ENST00000394105 12.19 1.24 4.05 1.67 3.99 3.75 0.60 0.27 0.23
BTK ENST00000308731 4.40 1.15 1.03 3.72 3.99 4.45 0.30 0.28 0.21
ARID1B ENST00000346085 23.46 1.25 9.89 1.37 3.99 2.30 1.09 0.27 0.41
PPFIA2 ENST00000549396 7.27 1.26 2.00 2.91 3.99 4.12 0.38 0.27 0.23
COPS2 ENST00000299259 0.84 1.26 0.17 4.36 3.98 4.85 0.18 0.27 0.18
COL1A1 ENST00000225964 11.83 1.27 3.90 1.64 3.98 3.76 0.60 0.27 0.23
DHX9 ENST00000367549 0.59 1.30 0.13 4.37 3.98 4.86 0.19 0.27 0.18
BIRC6 ENST00000421745 14.59 1.27 5.19 1.54 3.98 3.59 0.73 0.27 0.26
BAZ1B ENST00000339594 10.56 1.34 3.38 1.99 3.97 3.88 0.55 0.27 0.23
RALGAPB ENST00000262879 9.73 1.31 2.90 2.15 3.97 4.00 0.49 0.27 0.23
IPO7 ENST00000379719 6.56 1.28 1.78 3.00 3.97 4.24 0.37 0.27 0.23

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