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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
NXF1 ENST00000532297 15.37 12.18 11.46 1.56 2.09 2.21 0.76 0.58 0.45
STAU1 ENST00000371856 15.38 4.06 7.09 1.56 3.24 2.86 0.76 0.32 0.33
ANO3 ENST00000256737 15.38 40.03 25.84 1.56 0.63 1.01 0.76 1.68 1.24
EIF3L ENST00000412331 15.39 17.69 14.23 1.56 1.54 1.99 0.76 0.73 0.60
LRP12 ENST00000276654 15.39 9.34 9.89 1.56 2.48 2.30 0.76 0.49 0.41
AC007040.11 ENST00000606025 15.40 64.73 38.36 1.56 0.48 0.85 0.76 1.24 2.04
TRERF1 ENST00000372922 15.40 1.64 5.77 1.56 3.85 3.31 0.76 0.26 0.28
TACC1 ENST00000317827 15.41 29.80 20.74 1.56 1.13 1.46 0.76 1.40 0.88
ETS2 ENST00000360214 15.41 5.37 7.78 1.56 3.07 2.66 0.76 0.32 0.33
SGK1 ENST00000367858 15.42 25.71 18.48 1.56 1.24 1.62 0.76 1.05 0.81
PLAGL2 ENST00000246229 15.42 8.40 9.37 1.56 2.53 2.29 0.76 0.46 0.39
LY6G5C ENST00000383237 15.43 59.75 35.71 1.54 0.52 0.85 0.76 1.37 1.77
CHAF1A ENST00000301280 15.43 1.84 5.89 1.54 3.78 3.30 0.76 0.26 0.29
CTPS2 ENST00000443824 15.44 18.27 14.57 1.56 1.48 1.97 0.76 0.74 0.59
CALB1 ENST00000265431 15.44 24.86 18.11 1.56 1.33 1.67 0.76 1.06 0.78
FAM222B ENST00000341217 15.45 32.52 22.08 1.56 0.86 1.15 0.76 1.49 0.96
SOX1 ENST00000330949 15.45 52.39 32.10 1.56 0.62 0.90 0.76 1.83 1.60
NOS1 ENST00000338101 15.46 6.00 8.09 1.56 2.82 2.59 0.76 0.35 0.37
VPS26B ENST00000281187 15.46 14.16 12.38 1.56 2.07 2.23 0.76 0.60 0.50
CHEK1 ENST00000534070 15.47 48.08 29.95 1.56 0.63 0.86 0.76 1.99 1.46
MALT1 ENST00000348428 15.47 10.39 10.51 1.56 2.24 2.19 0.76 0.50 0.43
VPS45 ENST00000369130 15.48 34.11 22.96 1.56 0.84 1.19 0.76 1.53 0.98
FGD4 ENST00000427716 15.48 22.10 16.63 1.54 1.51 1.71 0.76 0.83 0.70
TTYH3 ENST00000258796 15.49 6.51 8.36 1.54 2.63 2.53 0.76 0.37 0.37
MAPKBP1 ENST00000456763 15.50 20.52 15.83 1.54 1.43 1.77 0.76 0.78 0.66

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