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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
INTS1 ENST00000404767 36.29 20.72 26.67 0.97 1.46 0.99 1.82 0.81 1.26
PLK4 ENST00000270861 36.29 29.56 31.11 0.97 1.10 0.84 1.82 1.39 1.53
FAM178A ENST00000370269 36.30 27.30 29.98 0.97 1.25 0.85 1.82 1.15 1.46
MASTL ENST00000375940 36.30 51.72 42.27 0.97 0.61 0.70 1.82 1.88 2.01
MRPS35 ENST00000081029 36.31 68.85 51.73 0.97 0.54 0.62 1.83 1.18 1.93
DCBLD1 ENST00000296955 36.32 43.08 37.97 0.97 0.61 0.85 1.83 1.91 2.02
IGFBP3 ENST00000381083 36.32 18.04 25.24 0.97 1.52 1.05 1.83 0.74 1.15
AJAP1 ENST00000378191 36.33 5.42 18.87 0.97 3.05 1.56 1.82 0.33 0.83
SBDS ENST00000246868 36.33 62.93 48.52 0.97 0.51 0.68 1.82 1.31 1.86
HBB ENST00000335295 36.34 97.35 68.88 0.97 0.23 0.46 1.82 0.19 1.04
PGM2 ENST00000381967 36.34 51.55 42.19 0.97 0.63 0.68 1.82 1.87 2.02
NHLRC2 ENST00000369301 36.35 36.59 34.71 0.97 0.78 0.90 1.82 1.63 1.75
SYNE1 ENST00000367255 36.35 19.45 26.07 0.96 1.44 0.99 1.82 0.74 1.25
CFB ENST00000425368 36.36 26.84 29.77 0.96 1.23 0.86 1.82 1.12 1.43
ARL6IP5 ENST00000273258 36.36 67.27 50.89 0.96 0.56 0.67 1.82 1.21 1.85
CFDP1 ENST00000283882 36.37 40.58 36.60 0.96 0.63 0.85 1.82 1.76 1.91
OAF ENST00000328965 36.37 65.61 49.97 0.96 0.53 0.61 1.81 1.22 1.90
RMI1 ENST00000325875 36.38 48.93 40.84 0.96 0.65 0.80 1.81 2.04 2.05
ANKS4B ENST00000311620 36.38 68.85 51.76 0.96 0.53 0.62 1.80 1.18 1.92
GMNN ENST00000230056 36.39 44.26 38.60 0.95 0.61 0.84 1.80 1.95 2.01
EIF3K ENST00000248342 36.39 45.33 39.25 0.95 0.68 0.78 1.80 1.98 2.04
SLC22A8 ENST00000336232 36.40 64.22 49.23 0.95 0.49 0.72 1.81 1.19 1.84
FOXO4 ENST00000374259 36.40 23.95 28.35 0.95 1.38 0.78 1.82 0.95 1.29
FAAH ENST00000243167 36.41 57.77 45.80 0.95 0.57 0.68 1.82 1.47 1.98
ARFRP1 ENST00000359715 36.41 33.08 32.92 0.95 0.84 0.86 1.81 1.49 1.66

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